From 114f6b0f80338f17b4fb94b8fff90a2d7ef9db89 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 14 Dec 2021 16:42:58 +0000 Subject: [PATCH 01/21] Template update for nf-core/tools version 2.2 --- .gitattributes | 2 + .github/CONTRIBUTING.md | 38 ++------ .github/ISSUE_TEMPLATE/bug_report.md | 63 ------------- .github/ISSUE_TEMPLATE/bug_report.yml | 52 ++++++++++ .github/ISSUE_TEMPLATE/config.yml | 1 - .github/ISSUE_TEMPLATE/feature_request.md | 32 ------- .github/ISSUE_TEMPLATE/feature_request.yml | 11 +++ .github/workflows/awsfulltest.yml | 8 +- .github/workflows/awstest.yml | 10 +- .github/workflows/ci.yml | 23 +++-- .github/workflows/linting_comment.yml | 1 + CHANGELOG.md | 2 +- CITATIONS.md | 2 +- README.md | 15 +-- assets/email_template.html | 2 +- assets/multiqc_config.yaml | 2 +- assets/nf-core-bacass_logo.png | Bin 18186 -> 0 bytes assets/nf-core-bacass_logo_light.png | Bin 0 -> 11313 bytes assets/sendmail_template.txt | 4 +- bin/scrape_software_versions.py | 36 ------- conf/base.config | 3 + conf/modules.config | 55 ++++++----- conf/test.config | 4 +- docs/images/nf-core-bacass_logo.png | Bin 34789 -> 0 bytes docs/images/nf-core-bacass_logo_dark.png | Bin 0 -> 71210 bytes docs/images/nf-core-bacass_logo_light.png | Bin 0 -> 71089 bytes docs/output.md | 2 +- docs/usage.md | 36 ------- lib/NfcoreSchema.groovy | 26 +++-- lib/NfcoreTemplate.groovy | 30 ++---- lib/Utils.groovy | 7 -- lib/WorkflowMain.groovy | 6 +- modules.json | 9 +- modules/local/functions.nf | 68 ------------- modules/local/get_software_versions.nf | 33 ------- modules/local/samplesheet_check.nf | 24 ++--- .../custom/dumpsoftwareversions/main.nf | 21 +++++ .../custom/dumpsoftwareversions/meta.yml | 34 +++++++ .../templates/dumpsoftwareversions.py | 89 ++++++++++++++++++ modules/nf-core/modules/fastqc/functions.nf | 68 ------------- modules/nf-core/modules/fastqc/main.nf | 39 ++++---- modules/nf-core/modules/fastqc/meta.yml | 7 +- modules/nf-core/modules/multiqc/functions.nf | 68 ------------- modules/nf-core/modules/multiqc/main.nf | 31 +++--- modules/nf-core/modules/multiqc/meta.yml | 7 +- nextflow.config | 35 +++---- nextflow_schema.json | 31 +----- subworkflows/local/input_check.nf | 8 +- workflows/bacass.nf | 44 +++------ 49 files changed, 414 insertions(+), 675 deletions(-) delete mode 100644 .github/ISSUE_TEMPLATE/bug_report.md create mode 100644 .github/ISSUE_TEMPLATE/bug_report.yml delete mode 100644 .github/ISSUE_TEMPLATE/feature_request.md create mode 100644 .github/ISSUE_TEMPLATE/feature_request.yml delete mode 100644 assets/nf-core-bacass_logo.png create mode 100644 assets/nf-core-bacass_logo_light.png delete mode 100755 bin/scrape_software_versions.py delete mode 100644 docs/images/nf-core-bacass_logo.png create mode 100644 docs/images/nf-core-bacass_logo_dark.png create mode 100644 docs/images/nf-core-bacass_logo_light.png delete mode 100644 modules/local/functions.nf delete mode 100644 modules/local/get_software_versions.nf create mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/main.nf create mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml create mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py delete mode 100644 modules/nf-core/modules/fastqc/functions.nf delete mode 100644 modules/nf-core/modules/multiqc/functions.nf diff --git a/.gitattributes b/.gitattributes index 7fe55006..050bb120 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1,3 @@ *.config linguist-language=nextflow +modules/nf-core/** linguist-generated +subworkflows/nf-core/** linguist-generated diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 42b647d0..3a3bca46 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -68,16 +68,13 @@ If you wish to contribute a new step, please use the following coding standards: 1. Define the corresponding input channel into your new process from the expected previous process channel 2. Write the process block (see below). 3. Define the output channel if needed (see below). -4. Add any new flags/options to `nextflow.config` with a default (see below). -5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`). -6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter). -7. Add sanity checks for all relevant parameters. -8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`. -9. Do local tests that the new code works properly and as expected. -10. Add a new test command in `.github/workflow/ci.yml`. -11. If applicable add a [MultiQC](https://https://multiqc.info/) module. -12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order. -13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`. +4. Add any new parameters to `nextflow.config` with a default (see below). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +6. Add sanity checks and validation for all relevant parameters. +7. Perform local tests to validate that the new code works as expected. +8. If applicable, add a new test command in `.github/workflow/ci.yml`. +9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. +10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. ### Default values @@ -102,27 +99,6 @@ Please use the following naming schemes, to make it easy to understand what is g If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` -### Software version reporting - -If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process. - -Add to the script block of the process, something like the following: - -```bash - --version &> v_.txt 2>&1 || true -``` - -or - -```bash - --help | head -n 1 &> v_.txt 2>&1 || true -``` - -You then need to edit the script `bin/scrape_software_versions.py` to: - -1. Add a Python regex for your tool's `--version` output (as in stored in the `v_.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1` -2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC. - ### Images and figures For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md deleted file mode 100644 index 8e0a6155..00000000 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ /dev/null @@ -1,63 +0,0 @@ ---- -name: Bug report -about: Report something that is broken or incorrect -labels: bug ---- - - - -## Check Documentation - -I have checked the following places for your error: - -- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) -- [ ] [nf-core/bacass pipeline documentation](https://nf-co.re/bacass/usage) - -## Description of the bug - - - -## Steps to reproduce - -Steps to reproduce the behaviour: - -1. Command line: -2. See error: - -## Expected behaviour - - - -## Log files - -Have you provided the following extra information/files: - -- [ ] The command used to run the pipeline -- [ ] The `.nextflow.log` file - -## System - -- Hardware: -- Executor: -- OS: -- Version - -## Nextflow Installation - -- Version: - -## Container engine - -- Engine: -- version: - -## Additional context - - diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml new file mode 100644 index 00000000..083ca89e --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -0,0 +1,52 @@ + +name: Bug report +description: Report something that is broken or incorrect +labels: bug +body: + + - type: markdown + attributes: + value: | + Before you post this issue, please check the documentation: + + - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) + - [nf-core/bacass pipeline documentation](https://nf-co.re/bacass/usage) + + - type: textarea + id: description + attributes: + label: Description of the bug + description: A clear and concise description of what the bug is. + validations: + required: true + + - type: textarea + id: command_used + attributes: + label: Command used and terminal output + description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal. + render: console + placeholder: | + $ nextflow run ... + + Some output where something broke + + - type: textarea + id: files + attributes: + label: Relevant files + description: | + Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed. + Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files. + + - type: textarea + id: system + attributes: + label: System information + description: | + * Nextflow version _(eg. 21.10.3)_ + * Hardware _(eg. HPC, Desktop, Cloud)_ + * Executor _(eg. slurm, local, awsbatch)_ + * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ + * OS _(eg. CentOS Linux, macOS, Linux Mint)_ + * Version of nf-core/bacass _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index eab75cde..02fa8097 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1,4 +1,3 @@ -blank_issues_enabled: false contact_links: - name: Join nf-core url: https://nf-co.re/join diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md deleted file mode 100644 index 29121dbd..00000000 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -name: Feature request -about: Suggest an idea for the nf-core/bacass pipeline -labels: enhancement ---- - - - -## Is your feature request related to a problem? Please describe - - - - - -## Describe the solution you'd like - - - -## Describe alternatives you've considered - - - -## Additional context - - diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml new file mode 100644 index 00000000..86e8463b --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -0,0 +1,11 @@ +name: Feature request +description: Suggest an idea for the nf-core/bacass pipeline +labels: enhancement +body: + - type: textarea + id: description + attributes: + label: Description of feature + description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered. + validations: + required: true diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index dac0a97d..0b9d2504 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,14 +14,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: nf-core/tower-action@master + uses: nf-core/tower-action@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }} + access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} pipeline: ${{ github.repository }} revision: ${{ github.sha }} @@ -30,5 +30,5 @@ jobs: { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-${{ github.sha }}" } - profiles: '[ "test_full", "aws_tower" ]' - + profiles: test_full,aws_tower + pre_run_script: 'export NXF_VER=21.10.3' diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 56b6ad8a..783627f6 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -11,18 +11,18 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: nf-core/tower-action@master + uses: nf-core/tower-action@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }} + access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} pipeline: ${{ github.repository }} revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bacass/work-${{ github.sha }} parameters: | { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-${{ github.sha }}" + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-test-${{ github.sha }}" } - profiles: '[ "test", "aws_tower" ]' - + profiles: test,aws_tower + pre_run_script: 'export NXF_VER=21.10.3' diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ef7bf59f..92ffd991 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -8,8 +8,9 @@ on: release: types: [published] -# Uncomment if we need an edge release of Nextflow again -# env: NXF_EDGE: 1 +env: + NXF_ANSI_LOG: false + CAPSULE_LOG: none jobs: test: @@ -17,20 +18,26 @@ jobs: # Only run on push if this is the nf-core dev branch (merged PRs) if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/bacass') }} runs-on: ubuntu-latest - env: - NXF_VER: ${{ matrix.nxf_ver }} - NXF_ANSI_LOG: false strategy: matrix: - # Nextflow versions: check pipeline minimum and current latest - nxf_ver: ['21.04.0', ''] + # Nextflow versions + include: + # Test pipeline minimum Nextflow version + - NXF_VER: '21.10.3' + NXF_EDGE: '' + # Test latest edge release of Nextflow + - NXF_VER: '' + NXF_EDGE: '1' steps: - name: Check out pipeline code uses: actions/checkout@v2 - name: Install Nextflow env: - CAPSULE_LOG: none + NXF_VER: ${{ matrix.NXF_VER }} + # Uncomment only if the edge release is more recent than the latest stable release + # See https://github.com/nextflow-io/nextflow/issues/2467 + # NXF_EDGE: ${{ matrix.NXF_EDGE }} run: | wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 90f03c6f..44d72994 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -15,6 +15,7 @@ jobs: uses: dawidd6/action-download-artifact@v2 with: workflow: linting.yml + workflow_conclusion: completed - name: Get PR number id: pr_number diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a649d99..3afacd9b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.1.1 - [date] +## v2.1.0dev - [date] Initial release of nf-core/bacass, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 6f36eb1e..48d05a82 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,7 @@ * [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/) +* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools diff --git a/README.md b/README.md index cbdd61c0..a64019d0 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@ -# ![nf-core/bacass](docs/images/nf-core-bacass_logo.png) +# ![nf-core/bacass](docs/images/nf-core-bacass_logo_light.png#gh-light-mode-only) ![nf-core/bacass](docs/images/nf-core-bacass_logo_dark.png#gh-dark-mode-only) [![GitHub Actions CI Status](https://github.com/nf-core/bacass/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/bacass/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/bacass/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/bacass/actions?query=workflow%3A%22nf-core+linting%22) [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/bacass/results) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -17,7 +17,7 @@ ## Introduction -**nf-core/bacass** is a bioinformatics best-practice analysis pipeline for Simple bacterial assembly and annotation pipeline.. +**nf-core/bacass** is a bioinformatics best-practice analysis pipeline for Simple bacterial assembly and annotation. The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! @@ -33,18 +33,21 @@ On release, automated continuous integration tests run the pipeline on a full-si ## Quick Start -1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.04.0`) +1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`) 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_ 3. Download the pipeline and test it on a minimal dataset with a single command: ```console - nextflow run nf-core/bacass -profile test, + nextflow run nf-core/bacass -profile test,YOURPROFILE ``` + Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. + + > * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > * If you are using `singularity` then the pipeline will auto-detect this and attempt to download the Singularity images directly as opposed to performing a conversion from Docker images. If you are persistently observing issues downloading Singularity images directly due to timeout or network issues then please use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, it is highly recommended to use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to pre-download all of the required containers before running the pipeline and to set the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options to be able to store and re-use the images from a central location for future pipeline runs. + > * If you are using `singularity` and are persistently observing issues downloading Singularity images directly due to timeout or network issues, then you can use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, you can use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. 4. Start running your own analysis! diff --git a/assets/email_template.html b/assets/email_template.html index 332ae36b..ebf8e7a3 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -4,7 +4,7 @@ - + nf-core/bacass Pipeline Report diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml index 0f3cd94d..228691b5 100644 --- a/assets/multiqc_config.yaml +++ b/assets/multiqc_config.yaml @@ -1,7 +1,7 @@ report_comment: > This report has been generated by the nf-core/bacass analysis pipeline. 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a/bin/scrape_software_versions.py +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env python -from __future__ import print_function -import os - -results = {} -version_files = [x for x in os.listdir(".") if x.endswith(".version.txt")] -for version_file in version_files: - - software = version_file.replace(".version.txt", "") - if software == "pipeline": - software = "nf-core/bacass" - - with open(version_file) as fin: - version = fin.read().strip() - results[software] = version - -# Dump to YAML -print( - """ -id: 'software_versions' -section_name: 'nf-core/bacass Software Versions' -section_href: 'https://github.com/nf-core/bacass' -plot_type: 'html' -description: 'are collected at run time from the software output.' -data: | -
-""" -) -for k, v in sorted(results.items()): - print("
{}
{}
".format(k, v)) -print("
") - -# Write out as tsv file: -with open("software_versions.tsv", "w") as f: - for k, v in sorted(results.items()): - f.write("{}\t{}\n".format(k, v)) diff --git a/conf/base.config b/conf/base.config index afa50340..dd6a7ad7 100644 --- a/conf/base.config +++ b/conf/base.config @@ -54,4 +54,7 @@ process { errorStrategy = 'retry' maxRetries = 2 } + withName:CUSTOM_DUMPSOFTWAREVERSIONS { + cache = false + } } diff --git a/conf/modules.config b/conf/modules.config index 0b1bfdec..a0506a4d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1,32 +1,41 @@ /* ======================================================================================== - Config file for defining DSL2 per module options + Config file for defining DSL2 per module options and publishing paths ======================================================================================== Available keys to override module options: - args = Additional arguments appended to command in module. - args2 = Second set of arguments appended to command in module (multi-tool modules). - args3 = Third set of arguments appended to command in module (multi-tool modules). - publish_dir = Directory to publish results. - publish_by_meta = Groovy list of keys available in meta map to append as directories to "publish_dir" path - If publish_by_meta = true - Value of ${meta['id']} is appended as a directory to "publish_dir" path - If publish_by_meta = ['id', 'custompath'] - If "id" is in meta map and "custompath" isn't then "${meta['id']}/custompath/" - is appended as a directory to "publish_dir" path - If publish_by_meta = false / null - No directories are appended to "publish_dir" path - publish_files = Groovy map where key = "file_ext" and value = "directory" to publish results for that file extension - The value of "directory" is appended to the standard "publish_dir" path as defined above. - If publish_files = null (unspecified) - All files are published. - If publish_files = false - No files are published. - suffix = File name suffix for output files. + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. ---------------------------------------------------------------------------------------- */ -params { - modules { - 'fastqc' { - args = "--quiet" - } - 'multiqc' { - args = "" - } +process { + + publishDir = [ + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: 'copy', + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + + withName: SAMPLESHEET_CHECK { + publishDir = [ + path: { "${params.outdir}/pipeline_info" }, + mode: 'copy', + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: FASTQC { + ext.args = '--quiet' } + + withName: CUSTOM_DUMPSOFTWAREVERSIONS { + publishDir = [ + path: { "${params.outdir}/pipeline_info" }, + mode: 'copy', + pattern: '*_versions.yml' + ] + } + } diff --git a/conf/test.config b/conf/test.config index 0d7c32bf..8401e6bc 100644 --- a/conf/test.config +++ b/conf/test.config @@ -16,8 +16,8 @@ params { // Limit resources so that this can run on GitHub Actions max_cpus = 2 - max_memory = 6.GB - max_time = 6.h + max_memory = '6.GB' + max_time = '6.h' // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets diff --git a/docs/images/nf-core-bacass_logo.png b/docs/images/nf-core-bacass_logo.png deleted file mode 100644 index d37cb23f55cfd9379c3e03773c145e22a877e2ae..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 34789 zcmYhi1yodBxIa9A(lJPPiL@XcLze>5Eezcq!qBOdfRfTB-QCjNT}ls)bk}!y@4f%^ zorTM_#EG-dexB!7J4{(o77Lve9RvbleRwaW3IZW&gFpx`P?3RuIq#Gk0scaBe6QmI 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zyTWN=Rb<%3Ty`H^SCPkLVusIUreF1x6cYXWfKC_*O|{(Ccw+;WxlUC+HQ-7B|Ja=O zmnRJ$GH}+eALIOiJ4DMA_z2-xIUtxf{O+)OZZff`>4|0W$rKmmxsKE>r`{7J?m_k~wIrC75#{{v+5up#Mh@7j zhs;1lgHZzC73OMiFk_d;M=fSWN&>L+V&RW869}2j%WGiah_MH=>sczd~J@Jn}Ht4Om*H#zIj_kF?L*?cf+7p!Y^n&6Md!(8gv zU+zHw!j4sQA;w{dmG_)dPx#teV_0X0sh%5_#-Gr~U+u9&X$ zS?e diff --git a/docs/usage.md b/docs/usage.md index b50bca2f..b116d5e0 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -181,42 +181,6 @@ process { > **NB:** We specify just the process name i.e. `STAR_ALIGN` in the config file and not the full task name string that is printed to screen in the error message or on the terminal whilst the pipeline is running i.e. `RNASEQ:ALIGN_STAR:STAR_ALIGN`. You may get a warning suggesting that the process selector isn't recognised but you can ignore that if the process name has been specified correctly. This is something that needs to be fixed upstream in core Nextflow. -### Tool-specific options - -For the ultimate flexibility, we have implemented and are using Nextflow DSL2 modules in a way where it is possible for both developers and users to change tool-specific command-line arguments (e.g. providing an additional command-line argument to the `STAR_ALIGN` process) as well as publishing options (e.g. saving files produced by the `STAR_ALIGN` process that aren't saved by default by the pipeline). In the majority of instances, as a user you won't have to change the default options set by the pipeline developer(s), however, there may be edge cases where creating a simple custom config file can improve the behaviour of the pipeline if for example it is failing due to a weird error that requires setting a tool-specific parameter to deal with smaller / larger genomes. - -The command-line arguments passed to STAR in the `STAR_ALIGN` module are a combination of: - -* Mandatory arguments or those that need to be evaluated within the scope of the module, as supplied in the [`script`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L49-L55) section of the module file. - -* An [`options.args`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L56) string of non-mandatory parameters that is set to be empty by default in the module but can be overwritten when including the module in the sub-workflow / workflow context via the `addParams` Nextflow option. - -The nf-core/rnaseq pipeline has a sub-workflow (see [terminology](https://github.com/nf-core/modules#terminology)) specifically to align reads with STAR and to sort, index and generate some basic stats on the resulting BAM files using SAMtools. At the top of this file we import the `STAR_ALIGN` module via the Nextflow [`include`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/subworkflows/nf-core/align_star.nf#L10) keyword and by default the options passed to the module via the `addParams` option are set as an empty Groovy map [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/subworkflows/nf-core/align_star.nf#L5); this in turn means `options.args` will be set to empty by default in the module file too. This is an intentional design choice and allows us to implement well-written sub-workflows composed of a chain of tools that by default run with the bare minimum parameter set for any given tool in order to make it much easier to share across pipelines and to provide the flexibility for users and developers to customise any non-mandatory arguments. - -When including the sub-workflow above in the main pipeline workflow we use the same `include` statement, however, we now have the ability to overwrite options for each of the tools in the sub-workflow including the [`align_options`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/workflows/rnaseq.nf#L225) variable that will be used specifically to overwrite the optional arguments passed to the `STAR_ALIGN` module. In this case, the options to be provided to `STAR_ALIGN` have been assigned sensible defaults by the developer(s) in the pipeline's [`modules.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/modules.config#L70-L74) and can be accessed and customised in the [workflow context](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/workflows/rnaseq.nf#L201-L204) too before eventually passing them to the sub-workflow as a Groovy map called `star_align_options`. These options will then be propagated from `workflow -> sub-workflow -> module`. - -As mentioned at the beginning of this section it may also be necessary for users to overwrite the options passed to modules to be able to customise specific aspects of the way in which a particular tool is executed by the pipeline. Given that all of the default module options are stored in the pipeline's `modules.config` as a [`params` variable](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/modules.config#L24-L25) it is also possible to overwrite any of these options via a custom config file. - -Say for example we want to append an additional, non-mandatory parameter (i.e. `--outFilterMismatchNmax 16`) to the arguments passed to the `STAR_ALIGN` module. Firstly, we need to copy across the default `args` specified in the [`modules.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/modules.config#L71) and create a custom config file that is a composite of the default `args` as well as the additional options you would like to provide. This is very important because Nextflow will overwrite the default value of `args` that you provide via the custom config. - -As you will see in the example below, we have: - -* appended `--outFilterMismatchNmax 16` to the default `args` used by the module. -* changed the default `publish_dir` value to where the files will eventually be published in the main results directory. -* appended `'bam':''` to the default value of `publish_files` so that the BAM files generated by the process will also be saved in the top-level results directory for the module. Note: `'out':'log'` means any file/directory ending in `out` will now be saved in a separate directory called `my_star_directory/log/`. - -```nextflow -params { - modules { - 'star_align' { - args = "--quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend --outFilterMismatchNmax 16" - publish_dir = "my_star_directory" - publish_files = ['out':'log', 'tab':'log', 'bam':''] - } - } -} -``` - ### Updating containers The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index 8d6920dd..40ab65f2 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -105,9 +105,13 @@ class NfcoreSchema { // Collect expected parameters from the schema def expectedParams = [] + def enums = [:] for (group in schemaParams) { for (p in group.value['properties']) { expectedParams.push(p.key) + if (group.value['properties'][p.key].containsKey('enum')) { + enums[p.key] = group.value['properties'][p.key]['enum'] + } } } @@ -155,7 +159,7 @@ class NfcoreSchema { println '' log.error 'ERROR: Validation of pipeline parameters failed!' JSONObject exceptionJSON = e.toJSON() - printExceptions(exceptionJSON, params_json, log) + printExceptions(exceptionJSON, params_json, log, enums) println '' has_error = true } @@ -202,7 +206,7 @@ class NfcoreSchema { } def type = '[' + group_params.get(param).type + ']' def description = group_params.get(param).description - def defaultValue = group_params.get(param).default ? " [default: " + group_params.get(param).default.toString() + "]" : '' + def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : '' def description_default = description + colors.dim + defaultValue + colors.reset // Wrap long description texts // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap @@ -260,13 +264,12 @@ class NfcoreSchema { // Get pipeline parameters defined in JSON Schema def Map params_summary = [:] - def blacklist = ['hostnames'] def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) for (group in params_map.keySet()) { def sub_params = new LinkedHashMap() def group_params = params_map.get(group) // This gets the parameters of that particular group for (param in group_params.keySet()) { - if (params.containsKey(param) && !blacklist.contains(param)) { + if (params.containsKey(param)) { def params_value = params.get(param) def schema_value = group_params.get(param).default def param_type = group_params.get(param).type @@ -330,7 +333,7 @@ class NfcoreSchema { // // Loop over nested exceptions and print the causingException // - private static void printExceptions(ex_json, params_json, log) { + private static void printExceptions(ex_json, params_json, log, enums, limit=5) { def causingExceptions = ex_json['causingExceptions'] if (causingExceptions.length() == 0) { def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/ @@ -346,11 +349,20 @@ class NfcoreSchema { else { def param = ex_json['pointerToViolation'] - ~/^#\// def param_val = params_json[param].toString() - log.error "* --${param}: ${ex_json['message']} (${param_val})" + if (enums.containsKey(param)) { + def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices" + if (enums[param].size() > limit) { + log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )" + } else { + log.error "${error_msg}: ${enums[param].join(', ')})" + } + } else { + log.error "* --${param}: ${ex_json['message']} (${param_val})" + } } } for (ex in causingExceptions) { - printExceptions(ex, params_json, log) + printExceptions(ex, params_json, log, enums) } } diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 44551e0a..2fc0a9b9 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -19,27 +19,16 @@ class NfcoreTemplate { } // - // Check params.hostnames + // Warn if a -profile or Nextflow config has not been provided to run the pipeline // - public static void hostName(workflow, params, log) { - Map colors = logColours(params.monochrome_logs) - if (params.hostnames) { - try { - def hostname = "hostname".execute().text.trim() - params.hostnames.each { prof, hnames -> - hnames.each { hname -> - if (hostname.contains(hname) && !workflow.profile.contains(prof)) { - log.info "=${colors.yellow}====================================================${colors.reset}=\n" + - "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" + - " but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" + - " ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" + - "=${colors.yellow}====================================================${colors.reset}=" - } - } - } - } catch (Exception e) { - log.warn "[$workflow.manifest.name] Could not determine 'hostname' - skipping check. Reason: ${e.message}." - } + public static void checkConfigProvided(workflow, log) { + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " } } @@ -168,7 +157,6 @@ class NfcoreTemplate { log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" } } else { - hostName(workflow, params, log) log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" } } diff --git a/lib/Utils.groovy b/lib/Utils.groovy index 18173e98..1b88aec0 100755 --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -37,11 +37,4 @@ class Utils { "===================================================================================" } } - - // - // Join module args with appropriate spacing - // - public static String joinModuleArgs(args_list) { - return ' ' + args_list.join(' ') - } } diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 6e61e6a5..2db15275 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -61,6 +61,9 @@ class WorkflowMain { // Print parameter summary log to screen log.info paramsSummaryLog(workflow, params, log) + // Check that a -profile or Nextflow config has been provided to run the pipeline + NfcoreTemplate.checkConfigProvided(workflow, log) + // Check that conda channels are set-up correctly if (params.enable_conda) { Utils.checkCondaChannels(log) @@ -69,9 +72,6 @@ class WorkflowMain { // Check AWS batch settings NfcoreTemplate.awsBatch(workflow, params) - // Check the hostnames against configured profiles - NfcoreTemplate.hostName(workflow, params, log) - // Check input has been provided if (!params.input) { log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'" diff --git a/modules.json b/modules.json index 7d548cca..b630d17f 100644 --- a/modules.json +++ b/modules.json @@ -3,12 +3,15 @@ "homePage": "https://github.com/nf-core/bacass", "repos": { "nf-core/modules": { + "custom/dumpsoftwareversions": { + "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41" + }, "fastqc": { - "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d" + "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961" }, "multiqc": { - "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d" + "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41" } } } -} +} \ No newline at end of file diff --git a/modules/local/functions.nf b/modules/local/functions.nf deleted file mode 100644 index da9da093..00000000 --- a/modules/local/functions.nf +++ /dev/null @@ -1,68 +0,0 @@ -// -// Utility functions used in nf-core DSL2 module files -// - -// -// Extract name of software tool from process name using $task.process -// -def getSoftwareName(task_process) { - return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() -} - -// -// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules -// -def initOptions(Map args) { - def Map options = [:] - options.args = args.args ?: '' - options.args2 = args.args2 ?: '' - options.args3 = args.args3 ?: '' - options.publish_by_meta = args.publish_by_meta ?: [] - options.publish_dir = args.publish_dir ?: '' - options.publish_files = args.publish_files - options.suffix = args.suffix ?: '' - return options -} - -// -// Tidy up and join elements of a list to return a path string -// -def getPathFromList(path_list) { - def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries - paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes - return paths.join('/') -} - -// -// Function to save/publish module results -// -def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) - } - } - } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } - } -} diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf deleted file mode 100644 index d7a9a92e..00000000 --- a/modules/local/get_software_versions.nf +++ /dev/null @@ -1,33 +0,0 @@ -// Import generic module functions -include { saveFiles } from './functions' - -params.options = [:] - -process GET_SOFTWARE_VERSIONS { - publishDir "${params.outdir}", - mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) } - - conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) - if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/python:3.8.3" - } else { - container "quay.io/biocontainers/python:3.8.3" - } - - cache false - - input: - path versions - - output: - path "software_versions.tsv" , emit: tsv - path 'software_versions_mqc.yaml', emit: yaml - - script: // This script is bundled with the pipeline, in nf-core/bacass/bin/ - """ - echo $workflow.manifest.version > pipeline.version.txt - echo $workflow.nextflow.version > nextflow.version.txt - scrape_software_versions.py &> software_versions_mqc.yaml - """ -} diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index e5ba91c2..322bd1e9 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -1,31 +1,27 @@ -// Import generic module functions -include { saveFiles } from './functions' - -params.options = [:] - process SAMPLESHEET_CHECK { tag "$samplesheet" - publishDir "${params.outdir}", - mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) } conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) - if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/python:3.8.3" - } else { - container "quay.io/biocontainers/python:3.8.3" - } + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.8.3' : + 'quay.io/biocontainers/python:3.8.3' }" input: path samplesheet output: - path '*.csv' + path '*.csv' , emit: csv + path "versions.yml", emit: versions script: // This script is bundled with the pipeline, in nf-core/bacass/bin/ """ check_samplesheet.py \\ $samplesheet \\ samplesheet.valid.csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + END_VERSIONS """ } diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf new file mode 100644 index 00000000..934bb467 --- /dev/null +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf @@ -0,0 +1,21 @@ +process CUSTOM_DUMPSOFTWAREVERSIONS { + label 'process_low' + + // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container + conda (params.enable_conda ? "bioconda::multiqc=1.11" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" + + input: + path versions + + output: + path "software_versions.yml" , emit: yml + path "software_versions_mqc.yml", emit: mqc_yml + path "versions.yml" , emit: versions + + script: + def args = task.ext.args ?: '' + template 'dumpsoftwareversions.py' +} diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml new file mode 100644 index 00000000..5b5b8a60 --- /dev/null +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml @@ -0,0 +1,34 @@ +name: custom_dumpsoftwareversions +description: Custom module used to dump software versions within the nf-core pipeline template +keywords: + - custom + - version +tools: + - custom: + description: Custom module used to dump software versions within the nf-core pipeline template + homepage: https://github.com/nf-core/tools + documentation: https://github.com/nf-core/tools + licence: ['MIT'] +input: + - versions: + type: file + description: YML file containing software versions + pattern: "*.yml" + +output: + - yml: + type: file + description: Standard YML file containing software versions + pattern: "software_versions.yml" + - mqc_yml: + type: file + description: MultiQC custom content YML file containing software versions + pattern: "software_versions_mqc.yml" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py new file mode 100644 index 00000000..d1390392 --- /dev/null +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -0,0 +1,89 @@ +#!/usr/bin/env python + +import yaml +import platform +from textwrap import dedent + + +def _make_versions_html(versions): + html = [ + dedent( + """\\ + + + + + + + + + + """ + ) + ] + for process, tmp_versions in sorted(versions.items()): + html.append("") + for i, (tool, version) in enumerate(sorted(tmp_versions.items())): + html.append( + dedent( + f"""\\ + + + + + + """ + ) + ) + html.append("") + html.append("
Process Name Software Version
{process if (i == 0) else ''}{tool}{version}
") + return "\\n".join(html) + + +versions_this_module = {} +versions_this_module["${task.process}"] = { + "python": platform.python_version(), + "yaml": yaml.__version__, +} + +with open("$versions") as f: + versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module + +# aggregate versions by the module name (derived from fully-qualified process name) +versions_by_module = {} +for process, process_versions in versions_by_process.items(): + module = process.split(":")[-1] + try: + assert versions_by_module[module] == process_versions, ( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) + except KeyError: + versions_by_module[module] = process_versions + +versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", + "$workflow.manifest.name": "$workflow.manifest.version", +} + +versions_mqc = { + "id": "software_versions", + "section_name": "${workflow.manifest.name} Software Versions", + "section_href": "https://github.com/${workflow.manifest.name}", + "plot_type": "html", + "description": "are collected at run time from the software output.", + "data": _make_versions_html(versions_by_module), +} + +with open("software_versions.yml", "w") as f: + yaml.dump(versions_by_module, f, default_flow_style=False) +with open("software_versions_mqc.yml", "w") as f: + yaml.dump(versions_mqc, f, default_flow_style=False) + +with open("versions.yml", "w") as f: + yaml.dump(versions_this_module, f, default_flow_style=False) diff --git a/modules/nf-core/modules/fastqc/functions.nf b/modules/nf-core/modules/fastqc/functions.nf deleted file mode 100644 index da9da093..00000000 --- a/modules/nf-core/modules/fastqc/functions.nf +++ /dev/null @@ -1,68 +0,0 @@ -// -// Utility functions used in nf-core DSL2 module files -// - -// -// Extract name of software tool from process name using $task.process -// -def getSoftwareName(task_process) { - return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() -} - -// -// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules -// -def initOptions(Map args) { - def Map options = [:] - options.args = args.args ?: '' - options.args2 = args.args2 ?: '' - options.args3 = args.args3 ?: '' - options.publish_by_meta = args.publish_by_meta ?: [] - options.publish_dir = args.publish_dir ?: '' - options.publish_files = args.publish_files - options.suffix = args.suffix ?: '' - return options -} - -// -// Tidy up and join elements of a list to return a path string -// -def getPathFromList(path_list) { - def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries - paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes - return paths.join('/') -} - -// -// Function to save/publish module results -// -def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) - } - } - } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } - } -} diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf index 39c327b2..d250eca0 100644 --- a/modules/nf-core/modules/fastqc/main.nf +++ b/modules/nf-core/modules/fastqc/main.nf @@ -1,22 +1,11 @@ -// Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' - -params.options = [:] -options = initOptions(params.options) - process FASTQC { tag "$meta.id" label 'process_medium' - publishDir "${params.outdir}", - mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) - if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0" - } else { - container "quay.io/biocontainers/fastqc:0.11.9--0" - } + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : + 'quay.io/biocontainers/fastqc:0.11.9--0' }" input: tuple val(meta), path(reads) @@ -24,24 +13,32 @@ process FASTQC { output: tuple val(meta), path("*.html"), emit: html tuple val(meta), path("*.zip") , emit: zip - path "*.version.txt" , emit: version + path "versions.yml" , emit: versions script: + def args = task.ext.args ?: '' // Add soft-links to original FastQs for consistent naming in pipeline - def software = getSoftwareName(task.process) - def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz - fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz - fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt + fastqc $args --threads $task.cpus ${prefix}.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS """ } else { """ [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz - fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz - fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt + fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS """ } } diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/modules/fastqc/meta.yml index 8eb9953d..b09553a3 100644 --- a/modules/nf-core/modules/fastqc/meta.yml +++ b/modules/nf-core/modules/fastqc/meta.yml @@ -15,6 +15,7 @@ tools: overrepresented sequences. homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ + licence: ['GPL-2.0-only'] input: - meta: type: map @@ -40,10 +41,10 @@ output: type: file description: FastQC report archive pattern: "*_{fastqc.zip}" - - version: + - versions: type: file - description: File containing software version - pattern: "*.{version.txt}" + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/modules/multiqc/functions.nf b/modules/nf-core/modules/multiqc/functions.nf deleted file mode 100644 index da9da093..00000000 --- a/modules/nf-core/modules/multiqc/functions.nf +++ /dev/null @@ -1,68 +0,0 @@ -// -// Utility functions used in nf-core DSL2 module files -// - -// -// Extract name of software tool from process name using $task.process -// -def getSoftwareName(task_process) { - return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() -} - -// -// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules -// -def initOptions(Map args) { - def Map options = [:] - options.args = args.args ?: '' - options.args2 = args.args2 ?: '' - options.args3 = args.args3 ?: '' - options.publish_by_meta = args.publish_by_meta ?: [] - options.publish_dir = args.publish_dir ?: '' - options.publish_files = args.publish_files - options.suffix = args.suffix ?: '' - return options -} - -// -// Tidy up and join elements of a list to return a path string -// -def getPathFromList(path_list) { - def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries - paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes - return paths.join('/') -} - -// -// Function to save/publish module results -// -def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) - } - } - } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } - } -} diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf index da780800..3dceb162 100644 --- a/modules/nf-core/modules/multiqc/main.nf +++ b/modules/nf-core/modules/multiqc/main.nf @@ -1,21 +1,10 @@ -// Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' - -params.options = [:] -options = initOptions(params.options) - process MULTIQC { label 'process_medium' - publishDir "${params.outdir}", - mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } - conda (params.enable_conda ? "bioconda::multiqc=1.10.1" : null) - if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/multiqc:1.10.1--py_0" - } else { - container "quay.io/biocontainers/multiqc:1.10.1--py_0" - } + conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" input: path multiqc_files @@ -24,12 +13,16 @@ process MULTIQC { path "*multiqc_report.html", emit: report path "*_data" , emit: data path "*_plots" , optional:true, emit: plots - path "*.version.txt" , emit: version + path "versions.yml" , emit: versions script: - def software = getSoftwareName(task.process) + def args = task.ext.args ?: '' """ - multiqc -f $options.args . - multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt + multiqc -f $args . + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS """ } diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/modules/multiqc/meta.yml index 532a8bb1..63c75a45 100644 --- a/modules/nf-core/modules/multiqc/meta.yml +++ b/modules/nf-core/modules/multiqc/meta.yml @@ -11,6 +11,7 @@ tools: It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ + licence: ['GPL-3.0-or-later'] input: - multiqc_files: type: file @@ -29,10 +30,10 @@ output: type: file description: Plots created by MultiQC pattern: "*_data" - - version: + - versions: type: file - description: File containing software version - pattern: "*.{version.txt}" + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/nextflow.config b/nextflow.config index d925a1a1..37ccbf49 100644 --- a/nextflow.config +++ b/nextflow.config @@ -26,7 +26,6 @@ params { // Boilerplate options outdir = './results' tracedir = "${params.outdir}/pipeline_info" - publish_dir_mode = 'copy' email = null email_on_fail = null plaintext_email = false @@ -34,14 +33,12 @@ params { help = false validate_params = true show_hidden_params = false - schema_ignore_params = 'genomes,modules' + schema_ignore_params = 'genomes' enable_conda = false - singularity_pull_docker_container = false // Config options custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - hostnames = [:] config_profile_description = null config_profile_contact = null config_profile_url = null @@ -58,9 +55,6 @@ params { // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' - // Load nf-core custom profiles from different Institutions try { includeConfig "${params.custom_config_base}/nfcore_custom.config" @@ -68,13 +62,6 @@ try { System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") } -// Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} - profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { @@ -126,11 +113,22 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Load igenomes.config if required +if (!params.igenomes_ignore) { + includeConfig 'conf/igenomes.config' +} else { + params.genomes = [:] +} + // Export these variables to prevent local Python/R libraries from conflicting with those in the container +// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. +// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. + env { PYTHONNOUSERSITE = 1 R_PROFILE_USER = "/.Rprofile" R_ENVIRON_USER = "/.Renviron" + JULIA_DEPOT_PATH = "/usr/local/share/julia" } // Capture exit codes from upstream processes when piping @@ -158,12 +156,15 @@ manifest { name = 'nf-core/bacass' author = 'Andreas Wilm, Alexander Peltzer' homePage = 'https://github.com/nf-core/bacass' - description = 'Simple bacterial assembly and annotation pipeline.' + description = 'Simple bacterial assembly and annotation' mainScript = 'main.nf' - nextflowVersion = '!>=21.04.0' - version = '1.1.1' + nextflowVersion = '!>=21.10.3' + version = '2.1.0dev' } +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' + // Function to ensure that resource requirements don't go beyond // a maximum limit def check_max(obj, type) { diff --git a/nextflow_schema.json b/nextflow_schema.json index 240d7591..8c91df60 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -2,7 +2,7 @@ "$schema": "http://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/bacass/master/nextflow_schema.json", "title": "nf-core/bacass pipeline parameters", - "description": "Simple bacterial assembly and annotation pipeline.", + "description": "Simple bacterial assembly and annotation", "type": "object", "definitions": { "input_output_options": { @@ -104,12 +104,6 @@ "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", "fa_icon": "fas fa-users-cog" }, - "hostnames": { - "type": "string", - "description": "Institutional configs hostname.", - "hidden": true, - "fa_icon": "fas fa-users-cog" - }, "config_profile_name": { "type": "string", "description": "Institutional config name.", @@ -184,22 +178,6 @@ "fa_icon": "fas fa-question-circle", "hidden": true }, - "publish_dir_mode": { - "type": "string", - "default": "copy", - "description": "Method used to save pipeline results to output directory.", - "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", - "fa_icon": "fas fa-copy", - "enum": [ - "symlink", - "rellink", - "link", - "copy", - "copyNoFollow", - "move" - ], - "hidden": true - }, "email_on_fail": { "type": "string", "description": "Email address for completion summary, only when pipeline fails.", @@ -260,13 +238,6 @@ "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.", "hidden": true, "fa_icon": "fas fa-bacon" - }, - "singularity_pull_docker_container": { - "type": "boolean", - "description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.", - "hidden": true, - "fa_icon": "fas fa-toolbox", - "help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues." } } } diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf index b664bc8c..cddcbb3c 100644 --- a/subworkflows/local/input_check.nf +++ b/subworkflows/local/input_check.nf @@ -2,9 +2,7 @@ // Check input samplesheet and get read channels // -params.options = [:] - -include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' addParams( options: params.options ) +include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' workflow INPUT_CHECK { take: @@ -12,12 +10,14 @@ workflow INPUT_CHECK { main: SAMPLESHEET_CHECK ( samplesheet ) + .csv .splitCsv ( header:true, sep:',' ) .map { create_fastq_channels(it) } .set { reads } emit: - reads // channel: [ val(meta), [ reads ] ] + reads // channel: [ val(meta), [ reads ] ] + versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] } // Function to get list of [ meta, [ fastq_1, fastq_2 ] ] diff --git a/workflows/bacass.nf b/workflows/bacass.nf index b00c86a5..60d70b47 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -32,18 +32,10 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi ======================================================================================== */ -// Don't overwrite global params.modules, create a copy instead and use that within the main script. -def modules = params.modules.clone() - -// -// MODULE: Local to the pipeline -// -include { GET_SOFTWARE_VERSIONS } from '../modules/local/get_software_versions' addParams( options: [publish_files : ['tsv':'']] ) - // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // -include { INPUT_CHECK } from '../subworkflows/local/input_check' addParams( options: [:] ) +include { INPUT_CHECK } from '../subworkflows/local/input_check' /* ======================================================================================== @@ -51,14 +43,12 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check' addParams( opti ======================================================================================== */ -def multiqc_options = modules['multiqc'] -multiqc_options.args += params.multiqc_title ? Utils.joinModuleArgs(["--title \"$params.multiqc_title\""]) : '' - // // MODULE: Installed directly from nf-core/modules // -include { FASTQC } from '../modules/nf-core/modules/fastqc/main' addParams( options: modules['fastqc'] ) -include { MULTIQC } from '../modules/nf-core/modules/multiqc/main' addParams( options: multiqc_options ) +include { FASTQC } from '../modules/nf-core/modules/fastqc/main' +include { MULTIQC } from '../modules/nf-core/modules/multiqc/main' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' /* ======================================================================================== @@ -71,7 +61,7 @@ def multiqc_report = [] workflow BACASS { - ch_software_versions = Channel.empty() + ch_versions = Channel.empty() // // SUBWORKFLOW: Read in samplesheet, validate and stage input files @@ -79,6 +69,7 @@ workflow BACASS { INPUT_CHECK ( ch_input ) + ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) // // MODULE: Run FastQC @@ -86,21 +77,10 @@ workflow BACASS { FASTQC ( INPUT_CHECK.out.reads ) - ch_software_versions = ch_software_versions.mix(FASTQC.out.version.first().ifEmpty(null)) + ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - // - // MODULE: Pipeline reporting - // - ch_software_versions - .map { it -> if (it) [ it.baseName, it ] } - .groupTuple() - .map { it[1][0] } - .flatten() - .collect() - .set { ch_software_versions } - - GET_SOFTWARE_VERSIONS ( - ch_software_versions.map { it }.collect() + CUSTOM_DUMPSOFTWAREVERSIONS ( + ch_versions.unique().collectFile(name: 'collated_versions.yml') ) // @@ -113,14 +93,14 @@ workflow BACASS { ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config)) ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(GET_SOFTWARE_VERSIONS.out.yaml.collect()) + ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) MULTIQC ( ch_multiqc_files.collect() ) - multiqc_report = MULTIQC.out.report.toList() - ch_software_versions = ch_software_versions.mix(MULTIQC.out.version.ifEmpty(null)) + multiqc_report = MULTIQC.out.report.toList() + ch_versions = ch_versions.mix(MULTIQC.out.versions) } /* From 3b846baeb2fd123f64852221b7453d57b0bd1cd9 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 15 Mar 2022 20:58:18 +0000 Subject: [PATCH 02/21] Template update for nf-core/tools version 2.3 --- .github/ISSUE_TEMPLATE/bug_report.yml | 1 - .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 6 +- .github/workflows/awstest.yml | 6 +- .github/workflows/ci.yml | 4 +- .github/workflows/linting.yml | 28 +-- .gitpod.yml | 14 ++ .nf-core.yml | 1 + .yamllint.yml | 6 + README.md | 6 +- bin/check_samplesheet.py | 346 +++++++++++++++++--------- conf/base.config | 4 +- conf/igenomes.config | 80 +++--- conf/modules.config | 18 +- conf/test.config | 6 +- conf/test_full.config | 6 +- docs/usage.md | 21 +- lib/NfcoreSchema.groovy | 4 +- lib/Utils.groovy | 4 +- lib/WorkflowBacass.groovy | 4 +- main.nf | 24 +- nextflow.config | 18 +- nextflow_schema.json | 23 +- subworkflows/local/input_check.nf | 18 +- workflows/bacass.nf | 28 +-- 25 files changed, 419 insertions(+), 259 deletions(-) create mode 100644 .gitpod.yml create mode 100644 .nf-core.yml create mode 100644 .yamllint.yml diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 083ca89e..5379c092 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -1,4 +1,3 @@ - name: Bug report description: Report something that is broken or incorrect labels: bug diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index dcccebd8..31d57c86 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/baca - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`). +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 0b9d2504..7655d02a 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: nf-core/tower-action@v2 + uses: nf-core/tower-action@v3 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -31,4 +31,6 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-${{ github.sha }}" } profiles: test_full,aws_tower - pre_run_script: 'export NXF_VER=21.10.3' + nextflow_config: | + process.errorStrategy = 'retry' + process.maxRetries = 3 diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 783627f6..eda5d710 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: nf-core/tower-action@v2 + uses: nf-core/tower-action@v3 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} @@ -25,4 +25,6 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-test-${{ github.sha }}" } profiles: test,aws_tower - pre_run_script: 'export NXF_VER=21.10.3' + nextflow_config: | + process.errorStrategy = 'retry' + process.maxRetries = 3 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 92ffd991..ede529a7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -14,7 +14,7 @@ env: jobs: test: - name: Run workflow tests + name: Run pipeline with test data # Only run on push if this is the nf-core dev branch (merged PRs) if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/bacass') }} runs-on: ubuntu-latest @@ -47,4 +47,4 @@ jobs: # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 3b448773..fda934c0 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -12,9 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - uses: actions/setup-node@v1 - with: - node-version: '10' + - uses: actions/setup-node@v2 - name: Install markdownlint run: npm install -g markdownlint-cli - name: Run Markdownlint @@ -51,9 +49,7 @@ jobs: steps: - uses: actions/checkout@v2 - - uses: actions/setup-node@v1 - with: - node-version: '10' + - uses: actions/setup-node@v2 - name: Install editorconfig-checker run: npm install -g editorconfig-checker @@ -64,14 +60,13 @@ jobs: YAML: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 - - uses: actions/setup-node@v1 + - name: Checkout + uses: actions/checkout@master + - name: 'Yamllint' + uses: karancode/yamllint-github-action@master with: - node-version: '10' - - name: Install yaml-lint - run: npm install -g yaml-lint - - name: Run yaml-lint - run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") + yamllint_file_or_dir: '.' + yamllint_config_filepath: '.yamllint.yml' # If the above check failed, post a comment on the PR explaining the failure - name: Post PR comment @@ -84,10 +79,11 @@ jobs: To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run: - * Install `yaml-lint` - * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`) + * Install `yamllint` + * Install `yamllint` following [this](https://yamllint.readthedocs.io/en/stable/quickstart.html#installing-yamllint) + instructions or alternative install it in your [conda environment](https://anaconda.org/conda-forge/yamllint) * Fix the markdown errors - * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")` + * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml` * Fix any reported errors in your YAML files Once you push these changes the test should pass, and you can hide this comment :+1: diff --git a/.gitpod.yml b/.gitpod.yml new file mode 100644 index 00000000..b7d4cee1 --- /dev/null +++ b/.gitpod.yml @@ -0,0 +1,14 @@ +image: nfcore/gitpod:latest + +vscode: + extensions: # based on nf-core.nf-core-extensionpack + - codezombiech.gitignore # Language support for .gitignore files + # - cssho.vscode-svgviewer # SVG viewer + - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code + - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed + - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files + - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar + - mechatroner.rainbow-csv # Highlight columns in csv files in different colors + # - nextflow.nextflow # Nextflow syntax highlighting + - oderwat.indent-rainbow # Highlight indentation level + - streetsidesoftware.code-spell-checker # Spelling checker for source code diff --git a/.nf-core.yml b/.nf-core.yml new file mode 100644 index 00000000..3805dc81 --- /dev/null +++ b/.nf-core.yml @@ -0,0 +1 @@ +repository_type: pipeline diff --git a/.yamllint.yml b/.yamllint.yml new file mode 100644 index 00000000..d466deec --- /dev/null +++ b/.yamllint.yml @@ -0,0 +1,6 @@ +extends: default + +rules: + document-start: disable + line-length: disable + truthy: disable diff --git a/README.md b/README.md index a64019d0..f10e90d1 100644 --- a/README.md +++ b/README.md @@ -40,14 +40,14 @@ On release, automated continuous integration tests run the pipeline on a full-si 3. Download the pipeline and test it on a minimal dataset with a single command: ```console - nextflow run nf-core/bacass -profile test,YOURPROFILE + nextflow run nf-core/bacass -profile test,YOURPROFILE --outdir ``` Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. > * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > * If you are using `singularity` and are persistently observing issues downloading Singularity images directly due to timeout or network issues, then you can use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, you can use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. + > * If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. 4. Start running your own analysis! @@ -55,7 +55,7 @@ On release, automated continuous integration tests run the pipeline on a full-si ```console - nextflow run nf-core/bacass -profile --input samplesheet.csv --genome GRCh37 + nextflow run nf-core/bacass --input samplesheet.csv --outdir --genome GRCh37 -profile ``` ## Documentation diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index cef3e4fe..5473b624 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -1,145 +1,249 @@ #!/usr/bin/env python -# TODO nf-core: Update the script to check the samplesheet -# This script is based on the example at: https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv -import os -import sys -import errno +"""Provide a command line tool to validate and transform tabular samplesheets.""" + + import argparse +import csv +import logging +import sys +from collections import Counter +from pathlib import Path -def parse_args(args=None): - Description = "Reformat nf-core/bacass samplesheet file and check its contents." - Epilog = "Example usage: python check_samplesheet.py " +logger = logging.getLogger() - parser = argparse.ArgumentParser(description=Description, epilog=Epilog) - parser.add_argument("FILE_IN", help="Input samplesheet file.") - parser.add_argument("FILE_OUT", help="Output file.") - return parser.parse_args(args) +class RowChecker: + """ + Define a service that can validate and transform each given row. -def make_dir(path): - if len(path) > 0: - try: - os.makedirs(path) - except OSError as exception: - if exception.errno != errno.EEXIST: - raise exception + Attributes: + modified (list): A list of dicts, where each dict corresponds to a previously + validated and transformed row. The order of rows is maintained. + """ -def print_error(error, context="Line", context_str=""): - error_str = "ERROR: Please check samplesheet -> {}".format(error) - if context != "" and context_str != "": - error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format( - error, context.strip(), context_str.strip() + VALID_FORMATS = ( + ".fq.gz", + ".fastq.gz", + ) + + def __init__( + self, + sample_col="sample", + first_col="fastq_1", + second_col="fastq_2", + single_col="single_end", + **kwargs, + ): + """ + Initialize the row checker with the expected column names. + + Args: + sample_col (str): The name of the column that contains the sample name + (default "sample"). + first_col (str): The name of the column that contains the first (or only) + FASTQ file path (default "fastq_1"). + second_col (str): The name of the column that contains the second (if any) + FASTQ file path (default "fastq_2"). + single_col (str): The name of the new column that will be inserted and + records whether the sample contains single- or paired-end sequencing + reads (default "single_end"). + + """ + super().__init__(**kwargs) + self._sample_col = sample_col + self._first_col = first_col + self._second_col = second_col + self._single_col = single_col + self._seen = set() + self.modified = [] + + def validate_and_transform(self, row): + """ + Perform all validations on the given row and insert the read pairing status. + + Args: + row (dict): A mapping from column headers (keys) to elements of that row + (values). + + """ + self._validate_sample(row) + self._validate_first(row) + self._validate_second(row) + self._validate_pair(row) + self._seen.add((row[self._sample_col], row[self._first_col])) + self.modified.append(row) + + def _validate_sample(self, row): + """Assert that the sample name exists and convert spaces to underscores.""" + assert len(row[self._sample_col]) > 0, "Sample input is required." + # Sanitize samples slightly. + row[self._sample_col] = row[self._sample_col].replace(" ", "_") + + def _validate_first(self, row): + """Assert that the first FASTQ entry is non-empty and has the right format.""" + assert len(row[self._first_col]) > 0, "At least the first FASTQ file is required." + self._validate_fastq_format(row[self._first_col]) + + def _validate_second(self, row): + """Assert that the second FASTQ entry has the right format if it exists.""" + if len(row[self._second_col]) > 0: + self._validate_fastq_format(row[self._second_col]) + + def _validate_pair(self, row): + """Assert that read pairs have the same file extension. Report pair status.""" + if row[self._first_col] and row[self._second_col]: + row[self._single_col] = False + assert ( + Path(row[self._first_col]).suffixes == Path(row[self._second_col]).suffixes + ), "FASTQ pairs must have the same file extensions." + else: + row[self._single_col] = True + + def _validate_fastq_format(self, filename): + """Assert that a given filename has one of the expected FASTQ extensions.""" + assert any(filename.endswith(extension) for extension in self.VALID_FORMATS), ( + f"The FASTQ file has an unrecognized extension: {filename}\n" + f"It should be one of: {', '.join(self.VALID_FORMATS)}" ) - print(error_str) - sys.exit(1) + def validate_unique_samples(self): + """ + Assert that the combination of sample name and FASTQ filename is unique. + + In addition to the validation, also rename the sample if more than one sample, + FASTQ file combination exists. + + """ + assert len(self._seen) == len(self.modified), "The pair of sample name and FASTQ must be unique." + if len({pair[0] for pair in self._seen}) < len(self._seen): + counts = Counter(pair[0] for pair in self._seen) + seen = Counter() + for row in self.modified: + sample = row[self._sample_col] + seen[sample] += 1 + if counts[sample] > 1: + row[self._sample_col] = f"{sample}_T{seen[sample]}" + + +def sniff_format(handle): + """ + Detect the tabular format. + + Args: + handle (text file): A handle to a `text file`_ object. The read position is + expected to be at the beginning (index 0). + + Returns: + csv.Dialect: The detected tabular format. + + .. _text file: + https://docs.python.org/3/glossary.html#term-text-file -# TODO nf-core: Update the check_samplesheet function -def check_samplesheet(file_in, file_out): """ - This function checks that the samplesheet follows the following structure: + peek = handle.read(2048) + sniffer = csv.Sniffer() + if not sniffer.has_header(peek): + logger.critical(f"The given sample sheet does not appear to contain a header.") + sys.exit(1) + dialect = sniffer.sniff(peek) + handle.seek(0) + return dialect - sample,fastq_1,fastq_2 - SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz - SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz - SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, - For an example see: - https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv +def check_samplesheet(file_in, file_out): """ + Check that the tabular samplesheet has the structure expected by nf-core pipelines. - sample_mapping_dict = {} - with open(file_in, "r") as fin: + Validate the general shape of the table, expected columns, and each row. Also add + an additional column which records whether one or two FASTQ reads were found. - ## Check header - MIN_COLS = 2 - # TODO nf-core: Update the column names for the input samplesheet - HEADER = ["sample", "fastq_1", "fastq_2"] - header = [x.strip('"') for x in fin.readline().strip().split(",")] - if header[: len(HEADER)] != HEADER: - print("ERROR: Please check samplesheet header -> {} != {}".format(",".join(header), ",".join(HEADER))) - sys.exit(1) + Args: + file_in (pathlib.Path): The given tabular samplesheet. The format can be either + CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. + file_out (pathlib.Path): Where the validated and transformed samplesheet should + be created; always in CSV format. - ## Check sample entries - for line in fin: - lspl = [x.strip().strip('"') for x in line.strip().split(",")] - - # Check valid number of columns per row - if len(lspl) < len(HEADER): - print_error( - "Invalid number of columns (minimum = {})!".format(len(HEADER)), - "Line", - line, - ) - num_cols = len([x for x in lspl if x]) - if num_cols < MIN_COLS: - print_error( - "Invalid number of populated columns (minimum = {})!".format(MIN_COLS), - "Line", - line, - ) - - ## Check sample name entries - sample, fastq_1, fastq_2 = lspl[: len(HEADER)] - sample = sample.replace(" ", "_") - if not sample: - print_error("Sample entry has not been specified!", "Line", line) - - ## Check FastQ file extension - for fastq in [fastq_1, fastq_2]: - if fastq: - if fastq.find(" ") != -1: - print_error("FastQ file contains spaces!", "Line", line) - if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"): - print_error( - "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!", - "Line", - line, - ) - - ## Auto-detect paired-end/single-end - sample_info = [] ## [single_end, fastq_1, fastq_2] - if sample and fastq_1 and fastq_2: ## Paired-end short reads - sample_info = ["0", fastq_1, fastq_2] - elif sample and fastq_1 and not fastq_2: ## Single-end short reads - sample_info = ["1", fastq_1, fastq_2] - else: - print_error("Invalid combination of columns provided!", "Line", line) - - ## Create sample mapping dictionary = { sample: [ single_end, fastq_1, fastq_2 ] } - if sample not in sample_mapping_dict: - sample_mapping_dict[sample] = [sample_info] - else: - if sample_info in sample_mapping_dict[sample]: - print_error("Samplesheet contains duplicate rows!", "Line", line) - else: - sample_mapping_dict[sample].append(sample_info) - - ## Write validated samplesheet with appropriate columns - if len(sample_mapping_dict) > 0: - out_dir = os.path.dirname(file_out) - make_dir(out_dir) - with open(file_out, "w") as fout: - fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n") - for sample in sorted(sample_mapping_dict.keys()): - - ## Check that multiple runs of the same sample are of the same datatype - if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]): - print_error("Multiple runs of a sample must be of the same datatype!", "Sample: {}".format(sample)) - - for idx, val in enumerate(sample_mapping_dict[sample]): - fout.write(",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n") - else: - print_error("No entries to process!", "Samplesheet: {}".format(file_in)) - - -def main(args=None): - args = parse_args(args) - check_samplesheet(args.FILE_IN, args.FILE_OUT) + Example: + This function checks that the samplesheet follows the following structure, + see also the `viral recon samplesheet`_:: + + sample,fastq_1,fastq_2 + SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz + SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz + SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, + + .. _viral recon samplesheet: + https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv + + """ + required_columns = {"sample", "fastq_1", "fastq_2"} + # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. + with file_in.open(newline="") as in_handle: + reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) + # Validate the existence of the expected header columns. + if not required_columns.issubset(reader.fieldnames): + logger.critical(f"The sample sheet **must** contain the column headers: {', '.join(required_columns)}.") + sys.exit(1) + # Validate each row. + checker = RowChecker() + for i, row in enumerate(reader): + try: + checker.validate_and_transform(row) + except AssertionError as error: + logger.critical(f"{str(error)} On line {i + 2}.") + sys.exit(1) + checker.validate_unique_samples() + header = list(reader.fieldnames) + header.insert(1, "single_end") + # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. + with file_out.open(mode="w", newline="") as out_handle: + writer = csv.DictWriter(out_handle, header, delimiter=",") + writer.writeheader() + for row in checker.modified: + writer.writerow(row) + + +def parse_args(argv=None): + """Define and immediately parse command line arguments.""" + parser = argparse.ArgumentParser( + description="Validate and transform a tabular samplesheet.", + epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", + ) + parser.add_argument( + "file_in", + metavar="FILE_IN", + type=Path, + help="Tabular input samplesheet in CSV or TSV format.", + ) + parser.add_argument( + "file_out", + metavar="FILE_OUT", + type=Path, + help="Transformed output samplesheet in CSV format.", + ) + parser.add_argument( + "-l", + "--log-level", + help="The desired log level (default WARNING).", + choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), + default="WARNING", + ) + return parser.parse_args(argv) + + +def main(argv=None): + """Coordinate argument parsing and program execution.""" + args = parse_args(argv) + logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") + if not args.file_in.is_file(): + logger.error(f"The given input file {args.file_in} was not found!") + sys.exit(2) + args.file_out.parent.mkdir(parents=True, exist_ok=True) + check_samplesheet(args.file_in, args.file_out) if __name__ == "__main__": diff --git a/conf/base.config b/conf/base.config index dd6a7ad7..fb20f020 100644 --- a/conf/base.config +++ b/conf/base.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nf-core/bacass Nextflow base config file -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A 'blank slate' config file, appropriate for general use on most high performance compute environments. Assumes that all software is installed and available on the PATH. Runs in `local` mode - all jobs will be run on the logged in environment. diff --git a/conf/igenomes.config b/conf/igenomes.config index 855948de..7a1b3ac6 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for iGenomes paths -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Defines reference genomes using iGenome paths. Can be used by any config that customises the base path using: $params.igenomes_base / --igenomes_base @@ -13,7 +13,7 @@ params { genomes { 'GRCh37' { fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" @@ -26,7 +26,7 @@ params { } 'GRCh38' { fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" @@ -38,7 +38,7 @@ params { } 'GRCm38' { fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" @@ -51,7 +51,7 @@ params { } 'TAIR10' { fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" @@ -62,7 +62,7 @@ params { } 'EB2' { fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" @@ -72,7 +72,7 @@ params { } 'UMD3.1' { fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" @@ -83,7 +83,7 @@ params { } 'WBcel235' { fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" @@ -94,7 +94,7 @@ params { } 'CanFam3.1' { fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" @@ -105,7 +105,7 @@ params { } 'GRCz10' { fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" @@ -115,7 +115,7 @@ params { } 'BDGP6' { fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" @@ -126,7 +126,7 @@ params { } 'EquCab2' { fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" @@ -137,7 +137,7 @@ params { } 'EB1' { fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" @@ -147,7 +147,7 @@ params { } 'Galgal4' { fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" @@ -157,7 +157,7 @@ params { } 'Gm01' { fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" @@ -167,7 +167,7 @@ params { } 'Mmul_1' { fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" @@ -178,7 +178,7 @@ params { } 'IRGSP-1.0' { fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" @@ -188,7 +188,7 @@ params { } 'CHIMP2.1.4' { fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" @@ -199,7 +199,7 @@ params { } 'Rnor_5.0' { fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" @@ -209,7 +209,7 @@ params { } 'Rnor_6.0' { fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" @@ -219,7 +219,7 @@ params { } 'R64-1-1' { fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" @@ -230,7 +230,7 @@ params { } 'EF2' { fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" @@ -242,7 +242,7 @@ params { } 'Sbi1' { fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" @@ -252,7 +252,7 @@ params { } 'Sscrofa10.2' { fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" @@ -263,7 +263,7 @@ params { } 'AGPv3' { fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" @@ -273,7 +273,7 @@ params { } 'hg38' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" @@ -285,7 +285,7 @@ params { } 'hg19' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" @@ -298,7 +298,7 @@ params { } 'mm10' { fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" @@ -311,7 +311,7 @@ params { } 'bosTau8' { fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" @@ -321,7 +321,7 @@ params { } 'ce10' { fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" @@ -333,7 +333,7 @@ params { } 'canFam3' { fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" @@ -344,7 +344,7 @@ params { } 'danRer10' { fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" @@ -355,7 +355,7 @@ params { } 'dm6' { fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" @@ -366,7 +366,7 @@ params { } 'equCab2' { fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" @@ -377,7 +377,7 @@ params { } 'galGal4' { fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" @@ -388,7 +388,7 @@ params { } 'panTro4' { fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" @@ -399,7 +399,7 @@ params { } 'rn6' { fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" @@ -409,7 +409,7 @@ params { } 'sacCer3' { fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" @@ -419,7 +419,7 @@ params { } 'susScr3' { fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" diff --git a/conf/modules.config b/conf/modules.config index a0506a4d..da58a5d8 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1,12 +1,12 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Config file for defining DSL2 per module options and publishing paths -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. ---------------------------------------------------------------------------------------- */ @@ -14,14 +14,14 @@ process { publishDir = [ path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, - mode: 'copy', + mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] withName: SAMPLESHEET_CHECK { publishDir = [ path: { "${params.outdir}/pipeline_info" }, - mode: 'copy', + mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } @@ -33,7 +33,7 @@ process { withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, - mode: 'copy', + mode: params.publish_dir_mode, pattern: '*_versions.yml' ] } diff --git a/conf/test.config b/conf/test.config index 8401e6bc..c0d23c95 100644 --- a/conf/test.config +++ b/conf/test.config @@ -1,11 +1,11 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running minimal tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run nf-core/bacass -profile test, + nextflow run nf-core/bacass -profile test, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_full.config b/conf/test_full.config index 1bac8cd3..d35a88b9 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -1,11 +1,11 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running full-size tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run nf-core/bacass -profile test_full, + nextflow run nf-core/bacass -profile test_full, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/docs/usage.md b/docs/usage.md index b116d5e0..e82d37aa 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```console -nextflow run nf-core/bacass --input samplesheet.csv --genome GRCh37 -profile docker +nextflow run nf-core/bacass --input samplesheet.csv --outdir --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -141,11 +141,11 @@ Whilst the default requirements set within the pipeline will hopefully work for For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue: ```console -[62/149eb0] NOTE: Process `RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) -Error executing process > 'RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' +[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) +Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' Caused by: - Process `RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) + Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) Command executed: STAR \ @@ -169,17 +169,24 @@ Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` ``` -To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so based on the search results the file we want is `modules/nf-core/software/star/align/main.nf`. If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. Providing you haven't set any other standard nf-core parameters to __cap__ the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. +To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). +We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/software/star/align/main.nf`. +If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). +The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. +The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. +Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. +The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. ```nextflow process { - withName: STAR_ALIGN { + withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' { memory = 100.GB } } ``` -> **NB:** We specify just the process name i.e. `STAR_ALIGN` in the config file and not the full task name string that is printed to screen in the error message or on the terminal whilst the pipeline is running i.e. `RNASEQ:ALIGN_STAR:STAR_ALIGN`. You may get a warning suggesting that the process selector isn't recognised but you can ignore that if the process name has been specified correctly. This is something that needs to be fixed upstream in core Nextflow. +> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. +> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. ### Updating containers diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index 40ab65f2..b3d092f8 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -27,7 +27,7 @@ class NfcoreSchema { /* groovylint-disable-next-line UnusedPrivateMethodParameter */ public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') { def has_error = false - //=====================================================================// + //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// // Check for nextflow core params and unexpected params def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') @@ -135,7 +135,7 @@ class NfcoreSchema { } } - //=====================================================================// + //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// // Validate parameters against the schema InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream() JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream)) diff --git a/lib/Utils.groovy b/lib/Utils.groovy index 1b88aec0..28567bd7 100755 --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -29,12 +29,12 @@ class Utils { conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults')) if (conda_check_failed) { - log.warn "=============================================================================\n" + + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" + " NB: The order of the channels matters!\n" + - "===================================================================================" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } } } diff --git a/lib/WorkflowBacass.groovy b/lib/WorkflowBacass.groovy index 94f7e96d..aa100683 100755 --- a/lib/WorkflowBacass.groovy +++ b/lib/WorkflowBacass.groovy @@ -48,11 +48,11 @@ class WorkflowBacass { // private static void genomeExistsError(params, log) { if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - log.error "=============================================================================\n" + + log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + " Currently, the available genome keys are:\n" + " ${params.genomes.keySet().join(", ")}\n" + - "===================================================================================" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" System.exit(1) } } diff --git a/main.nf b/main.nf index 09ddaab9..6b776dd9 100644 --- a/main.nf +++ b/main.nf @@ -1,8 +1,8 @@ #!/usr/bin/env nextflow /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nf-core/bacass -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/bacass Website: https://nf-co.re/bacass Slack : https://nfcore.slack.com/channels/bacass @@ -12,25 +12,25 @@ nextflow.enable.dsl = 2 /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GENOME PARAMETER VALUES -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ VALIDATE & PRINT PARAMETER SUMMARY -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ WorkflowMain.initialise(workflow, params, log) /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOW FOR PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ include { BACASS } from './workflows/bacass' @@ -43,9 +43,9 @@ workflow NFCORE_BACASS { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN ALL WORKFLOWS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -57,7 +57,7 @@ workflow { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ diff --git a/nextflow.config b/nextflow.config index 37ccbf49..dccfc2ba 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nf-core/bacass Nextflow config file -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Default config options for all compute environments ---------------------------------------------------------------------------------------- */ @@ -24,8 +24,9 @@ params { max_multiqc_email_size = '25.MB' // Boilerplate options - outdir = './results' + outdir = null tracedir = "${params.outdir}/pipeline_info" + publish_dir_mode = 'copy' email = null email_on_fail = null plaintext_email = false @@ -62,6 +63,15 @@ try { System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") } +// Load nf-core/bacass custom profiles from different institutions. +// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! +// try { +// includeConfig "${params.custom_config_base}/pipeline/bacass.config" +// } catch (Exception e) { +// System.err.println("WARNING: Could not load nf-core/config/bacass profiles: ${params.custom_config_base}/pipeline/bacass.config") +// } + + profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { @@ -121,7 +131,7 @@ if (!params.igenomes_ignore) { } // Export these variables to prevent local Python/R libraries from conflicting with those in the container -// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. +// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. env { diff --git a/nextflow_schema.json b/nextflow_schema.json index 8c91df60..0d4d7f78 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -11,7 +11,8 @@ "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", "required": [ - "input" + "input", + "outdir" ], "properties": { "input": { @@ -26,8 +27,8 @@ }, "outdir": { "type": "string", - "description": "Path to the output directory where the results will be saved.", - "default": "./results", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", "fa_icon": "fas fa-folder-open" }, "email": { @@ -178,6 +179,22 @@ "fa_icon": "fas fa-question-circle", "hidden": true }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ], + "hidden": true + }, "email_on_fail": { "type": "string", "description": "Email address for completion summary, only when pipeline fails.", diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf index cddcbb3c..0aecf87f 100644 --- a/subworkflows/local/input_check.nf +++ b/subworkflows/local/input_check.nf @@ -12,7 +12,7 @@ workflow INPUT_CHECK { SAMPLESHEET_CHECK ( samplesheet ) .csv .splitCsv ( header:true, sep:',' ) - .map { create_fastq_channels(it) } + .map { create_fastq_channel(it) } .set { reads } emit: @@ -21,22 +21,24 @@ workflow INPUT_CHECK { } // Function to get list of [ meta, [ fastq_1, fastq_2 ] ] -def create_fastq_channels(LinkedHashMap row) { +def create_fastq_channel(LinkedHashMap row) { + // create meta map def meta = [:] - meta.id = row.sample - meta.single_end = row.single_end.toBoolean() + meta.id = row.sample + meta.single_end = row.single_end.toBoolean() - def array = [] + // add path(s) of the fastq file(s) to the meta map + def fastq_meta = [] if (!file(row.fastq_1).exists()) { exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" } if (meta.single_end) { - array = [ meta, [ file(row.fastq_1) ] ] + fastq_meta = [ meta, [ file(row.fastq_1) ] ] } else { if (!file(row.fastq_2).exists()) { exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" } - array = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] + fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] } - return array + return fastq_meta } diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 60d70b47..47913e2a 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ VALIDATE INPUTS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) @@ -18,18 +18,18 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CONFIG FILES -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true) ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT LOCAL MODULES/SUBWORKFLOWS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -38,9 +38,9 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi include { INPUT_CHECK } from '../subworkflows/local/input_check' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT NF-CORE MODULES/SUBWORKFLOWS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -51,9 +51,9 @@ include { MULTIQC } from '../modules/nf-core/modules/multiqc include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN MAIN WORKFLOW -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // Info required for completion email and summary @@ -104,9 +104,9 @@ workflow BACASS { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ COMPLETION EMAIL AND SUMMARY -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow.onComplete { @@ -117,7 +117,7 @@ workflow.onComplete { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ From 3e5ae0db5e622abb9b5a6d8149144416102b4fd4 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 23 Mar 2022 13:47:26 +0000 Subject: [PATCH 03/21] Template update for nf-core/tools version 2.3.1 --- .editorconfig | 5 +- .github/CONTRIBUTING.md | 15 +- .github/ISSUE_TEMPLATE/bug_report.yml | 1 - .github/PULL_REQUEST_TEMPLATE.md | 6 +- .github/workflows/awsfulltest.yml | 1 - .github/workflows/awstest.yml | 2 +- .github/workflows/branch.yml | 5 +- .github/workflows/ci.yml | 12 +- .github/workflows/linting.yml | 85 ++--------- .github/workflows/linting_comment.yml | 3 +- .gitpod.yml | 16 +- .markdownlint.yml | 14 -- .prettierrc.yml | 1 + .yamllint.yml | 6 - CHANGELOG.md | 2 + CITATIONS.md | 27 ++-- README.md | 31 ++-- assets/email_template.html | 142 ++++++++++++------ assets/multiqc_config.yaml | 11 -- assets/multiqc_config.yml | 11 ++ assets/schema_input.json | 5 +- docs/README.md | 8 +- docs/output.md | 28 ++-- docs/usage.md | 109 +++++++------- modules.json | 8 +- .../custom/dumpsoftwareversions/main.nf | 3 + .../custom/dumpsoftwareversions/meta.yml | 2 +- modules/nf-core/modules/fastqc/main.nf | 3 + modules/nf-core/modules/fastqc/meta.yml | 90 +++++------ modules/nf-core/modules/multiqc/main.nf | 9 +- modules/nf-core/modules/multiqc/meta.yml | 66 ++++---- nextflow_schema.json | 14 +- workflows/bacass.nf | 2 +- 33 files changed, 361 insertions(+), 382 deletions(-) delete mode 100644 .markdownlint.yml create mode 100644 .prettierrc.yml delete mode 100644 .yamllint.yml delete mode 100644 assets/multiqc_config.yaml create mode 100644 assets/multiqc_config.yml diff --git a/.editorconfig b/.editorconfig index 95549501..b6b31907 100644 --- a/.editorconfig +++ b/.editorconfig @@ -8,12 +8,9 @@ trim_trailing_whitespace = true indent_size = 4 indent_style = space -[*.{yml,yaml}] +[*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 -[*.json] -insert_final_newline = unset - # These files are edited and tested upstream in nf-core/modules [/modules/nf-core/**] charset = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 3a3bca46..60f7799e 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -15,8 +15,7 @@ Contributions to the code are even more welcome ;) If you'd like to write some code for nf-core/bacass, the standard workflow is as follows: -1. Check that there isn't already an issue about your idea in the [nf-core/bacass issues](https://github.com/nf-core/bacass/issues) to avoid duplicating work - * If there isn't one already, please create one so that others know you're working on this +1. Check that there isn't already an issue about your idea in the [nf-core/bacass issues](https://github.com/nf-core/bacass/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/bacass repository](https://github.com/nf-core/bacass) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). @@ -49,9 +48,9 @@ These tests are run both with the latest available version of `Nextflow` and als :warning: Only in the unlikely and regretful event of a release happening with a bug. -* On your own fork, make a new branch `patch` based on `upstream/master`. -* Fix the bug, and bump version (X.Y.Z+1). -* A PR should be made on `master` from patch to directly this particular bug. +- On your own fork, make a new branch `patch` based on `upstream/master`. +- Fix the bug, and bump version (X.Y.Z+1). +- A PR should be made on `master` from patch to directly this particular bug. ## Getting help @@ -73,7 +72,7 @@ If you wish to contribute a new step, please use the following coding standards: 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. -9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. +9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. ### Default values @@ -92,8 +91,8 @@ The process resources can be passed on to the tool dynamically within the proces Please use the following naming schemes, to make it easy to understand what is going where. -* initial process channel: `ch_output_from_` -* intermediate and terminal channels: `ch__for_` +- initial process channel: `ch_output_from_` +- intermediate and terminal channels: `ch__for_` ### Nextflow version bumping diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 5379c092..527bcbd4 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -2,7 +2,6 @@ name: Bug report description: Report something that is broken or incorrect labels: bug body: - - type: markdown attributes: value: | diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 31d57c86..d4f73bf9 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -16,10 +16,10 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/baca - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md) - - [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. + - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md) + - [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir `). +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 7655d02a..4e7752bc 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -18,7 +18,6 @@ jobs: # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters - with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index eda5d710..e04a4be1 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -10,9 +10,9 @@ jobs: if: github.repository == 'nf-core/bacass' runs-on: ubuntu-latest steps: + # Launch workflow using Tower CLI tool action - name: Launch workflow via tower uses: nf-core/tower-action@v3 - with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 453a14f4..5ae4f83e 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,8 +13,7 @@ jobs: - name: Check PRs if: github.repository == 'nf-core/bacass' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/bacass ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] - + "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/bacass ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]" # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets @@ -43,4 +42,4 @@ jobs: Thanks again for your contribution! repo-token: ${{ secrets.GITHUB_TOKEN }} allow-repeats: false - +# diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ede529a7..c4e0a928 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,18 +16,18 @@ jobs: test: name: Run pipeline with test data # Only run on push if this is the nf-core dev branch (merged PRs) - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/bacass') }} + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/bacass') }}" runs-on: ubuntu-latest strategy: matrix: # Nextflow versions include: # Test pipeline minimum Nextflow version - - NXF_VER: '21.10.3' - NXF_EDGE: '' + - NXF_VER: "21.10.3" + NXF_EDGE: "" # Test latest edge release of Nextflow - - NXF_VER: '' - NXF_EDGE: '1' + - NXF_VER: "" + NXF_EDGE: "1" steps: - name: Check out pipeline code uses: actions/checkout@v2 @@ -48,3 +48,5 @@ jobs: # Remember that you can parallelise this by using strategy.matrix run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + +# diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index fda934c0..e9cf5de3 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,7 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines +# It runs the `nf-core lint` and markdown lint tests to ensure +# that the code meets the nf-core guidelines. on: push: pull_request: @@ -8,42 +9,6 @@ on: types: [published] jobs: - Markdown: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - uses: actions/setup-node@v2 - - name: Install markdownlint - run: npm install -g markdownlint-cli - - name: Run Markdownlint - run: markdownlint . - - # If the above check failed, post a comment on the PR explaining the failure - - name: Post PR comment - if: failure() - uses: mshick/add-pr-comment@v1 - with: - message: | - ## Markdown linting is failing - - To keep the code consistent with lots of contributors, we run automated code consistency checks. - To fix this CI test, please run: - - * Install `markdownlint-cli` - * On Mac: `brew install markdownlint-cli` - * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`) - * Fix the markdown errors - * Automatically: `markdownlint . --fix` - * Manually resolve anything left from `markdownlint .` - - Once you push these changes the test should pass, and you can hide this comment :+1: - - We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! - - Thanks again for your contribution! - repo-token: ${{ secrets.GITHUB_TOKEN }} - allow-repeats: false - EditorConfig: runs-on: ubuntu-latest steps: @@ -55,49 +20,24 @@ jobs: run: npm install -g editorconfig-checker - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) + run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') - YAML: + Prettier: runs-on: ubuntu-latest steps: - - name: Checkout - uses: actions/checkout@master - - name: 'Yamllint' - uses: karancode/yamllint-github-action@master - with: - yamllint_file_or_dir: '.' - yamllint_config_filepath: '.yamllint.yml' - - # If the above check failed, post a comment on the PR explaining the failure - - name: Post PR comment - if: failure() - uses: mshick/add-pr-comment@v1 - with: - message: | - ## YAML linting is failing - - To keep the code consistent with lots of contributors, we run automated code consistency checks. - To fix this CI test, please run: - - * Install `yamllint` - * Install `yamllint` following [this](https://yamllint.readthedocs.io/en/stable/quickstart.html#installing-yamllint) - instructions or alternative install it in your [conda environment](https://anaconda.org/conda-forge/yamllint) - * Fix the markdown errors - * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml` - * Fix any reported errors in your YAML files + - uses: actions/checkout@v2 - Once you push these changes the test should pass, and you can hide this comment :+1: + - uses: actions/setup-node@v2 - We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! + - name: Install Prettier + run: npm install -g prettier - Thanks again for your contribution! - repo-token: ${{ secrets.GITHUB_TOKEN }} - allow-repeats: false + - name: Run Prettier --check + run: prettier --check ${GITHUB_WORKSPACE} nf-core: runs-on: ubuntu-latest steps: - - name: Check out pipeline code uses: actions/checkout@v2 @@ -110,8 +50,8 @@ jobs: - uses: actions/setup-python@v1 with: - python-version: '3.6' - architecture: 'x64' + python-version: "3.6" + architecture: "x64" - name: Install dependencies run: | @@ -139,3 +79,4 @@ jobs: lint_results.md PR_number.txt +# diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 44d72994..91c487a1 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -1,4 +1,3 @@ - name: nf-core linting comment # This workflow is triggered after the linting action is complete # It posts an automated comment to the PR, even if the PR is coming from a fork @@ -27,4 +26,4 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} path: linting-logs/lint_results.md - +# diff --git a/.gitpod.yml b/.gitpod.yml index b7d4cee1..c452ee93 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -2,13 +2,13 @@ image: nfcore/gitpod:latest vscode: extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files + - codezombiech.gitignore # Language support for .gitignore files # - cssho.vscode-svgviewer # SVG viewer - - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code - - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - - mechatroner.rainbow-csv # Highlight columns in csv files in different colors + - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code + - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed + - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files + - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar + - mechatroner.rainbow-csv # Highlight columns in csv files in different colors # - nextflow.nextflow # Nextflow syntax highlighting - - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code + - oderwat.indent-rainbow # Highlight indentation level + - streetsidesoftware.code-spell-checker # Spelling checker for source code diff --git a/.markdownlint.yml b/.markdownlint.yml deleted file mode 100644 index 9e605fcf..00000000 --- a/.markdownlint.yml +++ /dev/null @@ -1,14 +0,0 @@ -# Markdownlint configuration file -default: true -line-length: false -ul-indent: - indent: 4 -no-duplicate-header: - siblings_only: true -no-inline-html: - allowed_elements: - - img - - p - - kbd - - details - - summary diff --git a/.prettierrc.yml b/.prettierrc.yml new file mode 100644 index 00000000..c81f9a76 --- /dev/null +++ b/.prettierrc.yml @@ -0,0 +1 @@ +printWidth: 120 diff --git a/.yamllint.yml b/.yamllint.yml deleted file mode 100644 index d466deec..00000000 --- a/.yamllint.yml +++ /dev/null @@ -1,6 +0,0 @@ -extends: default - -rules: - document-start: disable - line-length: disable - truthy: disable diff --git a/CHANGELOG.md b/CHANGELOG.md index 3afacd9b..c5db3c7f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ Initial release of nf-core/bacass, created with the [nf-core](https://nf-co.re/) ### `Fixed` +- Clarified conda usage and added an installation tutorial for Singularity since the one on Syllabs' website uses an outdate version of GO Compiler + ### `Dependencies` ### `Deprecated` diff --git a/CITATIONS.md b/CITATIONS.md index 48d05a82..e3a69e9b 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,23 +10,26 @@ ## Pipeline tools -* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools -* [Anaconda](https://anaconda.com) - > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. +- [Anaconda](https://anaconda.com) -* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/) - > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. + > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. -* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/) - > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671. +- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/) -* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. -* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) - > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. +- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/) + + > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671. + +- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + +- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/README.md b/README.md index f10e90d1..eccd8cf9 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# ![nf-core/bacass](docs/images/nf-core-bacass_logo_light.png#gh-light-mode-only) ![nf-core/bacass](docs/images/nf-core-bacass_logo_dark.png#gh-dark-mode-only) +# ![nf-core/bacass](docs/images/nf-core/bacass_logo_light.png#gh-light-mode-only) ![nf-core/bacass](docs/images/nf-core/bacass_logo_dark.png#gh-dark-mode-only) [![GitHub Actions CI Status](https://github.com/nf-core/bacass/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/bacass/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/bacass/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/bacass/actions?query=workflow%3A%22nf-core+linting%22) @@ -17,11 +17,13 @@ ## Introduction + **nf-core/bacass** is a bioinformatics best-practice analysis pipeline for Simple bacterial assembly and annotation. The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! + On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/bacass/results). ## Pipeline summary @@ -35,28 +37,28 @@ On release, automated continuous integration tests run the pipeline on a full-si 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`) -2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_ +2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. 3. Download the pipeline and test it on a minimal dataset with a single command: - ```console - nextflow run nf-core/bacass -profile test,YOURPROFILE --outdir - ``` + ```console + nextflow run nf-core/bacass -profile test,YOURPROFILE --outdir + ``` - Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. + Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. - > * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. - > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > * If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. - > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. + > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. + > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. + > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. + > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. 4. Start running your own analysis! - + - ```console - nextflow run nf-core/bacass --input samplesheet.csv --outdir --genome GRCh37 -profile - ``` + ```console + nextflow run nf-core/bacass --input samplesheet.csv --outdir --genome GRCh37 -profile + ``` ## Documentation @@ -82,6 +84,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: diff --git a/assets/email_template.html b/assets/email_template.html index ebf8e7a3..49c7405c 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -1,53 +1,111 @@ - - - - + + + + - - nf-core/bacass Pipeline Report - - -

+ + + nf-core/bacass Pipeline Report + + +
+ - +

nf-core/bacass v${version}

+

Run Name: $runName

-

nf-core/bacass v${version}

-

Run Name: $runName

- -<% if (!success){ - out << """ -
-

nf-core/bacass execution completed unsuccessfully!

+ <% if (!success){ out << """ +
+

nf-core/bacass execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: $exitStatus.

The full error message was:

- 
${errorReport}
-
- """ -} else { - out << """ -
+ 
${errorReport}
+
+ """ } else { out << """ +
nf-core/bacass execution completed successfully! -
- """ -} -%> +
+ """ } %> -

The workflow was completed at $dateComplete (duration: $duration)

-

The command used to launch the workflow was as follows:

-
$commandLine
+

The workflow was completed at $dateComplete (duration: $duration)

+

The command used to launch the workflow was as follows:

+ 
+$commandLine
-

Pipeline Configuration:

- - - <% out << summary.collect{ k,v -> "" }.join("\n") %> - -
$k
$v
+

Pipeline Configuration:

+ + + <% out << summary.collect{ k,v -> " + + + + + " }.join("\n") %> + +
+ $k + + 
$v
+
-

nf-core/bacass

-

https://github.com/nf-core/bacass

- -
- - +

nf-core/bacass

+

https://github.com/nf-core/bacass

+
+ diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml deleted file mode 100644 index 228691b5..00000000 --- a/assets/multiqc_config.yaml +++ /dev/null @@ -1,11 +0,0 @@ -report_comment: > - This report has been generated by the nf-core/bacass - analysis pipeline. For information about how to interpret these results, please see the - documentation. -report_section_order: - software_versions: - order: -1000 - nf-core-bacass-summary: - order: -1001 - -export_plots: true diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml new file mode 100644 index 00000000..c16e95ab --- /dev/null +++ b/assets/multiqc_config.yml @@ -0,0 +1,11 @@ +report_comment: > + This report has been generated by the nf-core/bacass + analysis pipeline. For information about how to interpret these results, please see the + documentation. +report_section_order: + software_versions: + order: -1000 + "nf-core-bacass-summary": + order: -1001 + +export_plots: true diff --git a/assets/schema_input.json b/assets/schema_input.json index 9d286b07..9146feaa 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -31,9 +31,6 @@ ] } }, - "required": [ - "sample", - "fastq_1" - ] + "required": ["sample", "fastq_1"] } } diff --git a/docs/README.md b/docs/README.md index 5fbf9904..cfb27a10 100644 --- a/docs/README.md +++ b/docs/README.md @@ -2,9 +2,9 @@ The nf-core/bacass documentation is split into the following pages: -* [Usage](usage.md) - * An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. -* [Output](output.md) - * An overview of the different results produced by the pipeline and how to interpret them. +- [Usage](usage.md) + - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. +- [Output](output.md) + - An overview of the different results produced by the pipeline and how to interpret them. You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re) diff --git a/docs/output.md b/docs/output.md index a72b5940..50ca899a 100644 --- a/docs/output.md +++ b/docs/output.md @@ -12,18 +12,18 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -* [FastQC](#fastqc) - Raw read QC -* [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline -* [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution +- [FastQC](#fastqc) - Raw read QC +- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline +- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC
Output files -* `fastqc/` - * `*_fastqc.html`: FastQC report containing quality metrics. - * `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. +- `fastqc/` + - `*_fastqc.html`: FastQC report containing quality metrics. + - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
@@ -42,10 +42,10 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
Output files -* `multiqc/` - * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. - * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. - * `multiqc_plots/`: directory containing static images from the report in various formats. +- `multiqc/` + - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. + - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. + - `multiqc_plots/`: directory containing static images from the report in various formats.
@@ -58,10 +58,10 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
Output files -* `pipeline_info/` - * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. - * Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. +- `pipeline_info/` + - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. + - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. + - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
diff --git a/docs/usage.md b/docs/usage.md index e82d37aa..a3982540 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -44,11 +44,11 @@ TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz, TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, ``` -| Column | Description | -|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| Column | Description | +| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | +| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```console -nextflow run nf-core/bacass --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run nf-core/bacass --input samplesheet.csv --outdir --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -65,9 +65,9 @@ This will launch the pipeline with the `docker` configuration profile. See below Note that the pipeline will create the following files in your working directory: ```console -work # Directory containing the nextflow working files -results # Finished results (configurable, see below) -.nextflow_log # Log file from Nextflow +work # Directory containing the nextflow working files + # Finished results in specified location (defined with --outdir) +.nextflow_log # Log file from Nextflow # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` @@ -106,25 +106,25 @@ They are loaded in sequence, so later profiles can overwrite earlier profiles. If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended. -* `docker` - * A generic configuration profile to be used with [Docker](https://docker.com/) -* `singularity` - * A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/) -* `podman` - * A generic configuration profile to be used with [Podman](https://podman.io/) -* `shifter` - * A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) -* `charliecloud` - * A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) -* `conda` - * A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. -* `test` - * A profile with a complete configuration for automated testing - * Includes links to test data so needs no other parameters +- `docker` + - A generic configuration profile to be used with [Docker](https://docker.com/) +- `singularity` + - A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/) +- `podman` + - A generic configuration profile to be used with [Podman](https://podman.io/) +- `shifter` + - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) +- `charliecloud` + - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) +- `conda` + - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. +- `test` + - A profile with a complete configuration for automated testing + - Includes links to test data so needs no other parameters ### `-resume` -Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. +Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files' contents as well. For more info about this parameter, see [this blog post](https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html). You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names. @@ -186,6 +186,7 @@ process { ``` > **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. +> > If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. ### Updating containers @@ -196,35 +197,35 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio 2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags) 3. Create the custom config accordingly: - * For Docker: - - ```nextflow - process { - withName: PANGOLIN { - container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` - - * For Singularity: - - ```nextflow - process { - withName: PANGOLIN { - container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` - - * For Conda: - - ```nextflow - process { - withName: PANGOLIN { - conda = 'bioconda::pangolin=3.0.5' - } - } - ``` + - For Docker: + + ```nextflow + process { + withName: PANGOLIN { + container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' + } + } + ``` + + - For Singularity: + + ```nextflow + process { + withName: PANGOLIN { + container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' + } + } + ``` + + - For Conda: + + ```nextflow + process { + withName: PANGOLIN { + conda = 'bioconda::pangolin=3.0.5' + } + } + ``` > **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch. diff --git a/modules.json b/modules.json index b630d17f..91697355 100644 --- a/modules.json +++ b/modules.json @@ -4,14 +4,14 @@ "repos": { "nf-core/modules": { "custom/dumpsoftwareversions": { - "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41" + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "fastqc": { - "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961" + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "multiqc": { - "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41" + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" } } } -} \ No newline at end of file +} diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf index 934bb467..327d5100 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf @@ -15,6 +15,9 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { path "software_versions_mqc.yml", emit: mqc_yml path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' template 'dumpsoftwareversions.py' diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml index 5b5b8a60..60b546a0 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml @@ -8,7 +8,7 @@ tools: description: Custom module used to dump software versions within the nf-core pipeline template homepage: https://github.com/nf-core/tools documentation: https://github.com/nf-core/tools - licence: ['MIT'] + licence: ["MIT"] input: - versions: type: file diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf index d250eca0..ed6b8c50 100644 --- a/modules/nf-core/modules/fastqc/main.nf +++ b/modules/nf-core/modules/fastqc/main.nf @@ -15,6 +15,9 @@ process FASTQC { tuple val(meta), path("*.zip") , emit: zip path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' // Add soft-links to original FastQs for consistent naming in pipeline diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/modules/fastqc/meta.yml index b09553a3..4da5bb5a 100644 --- a/modules/nf-core/modules/fastqc/meta.yml +++ b/modules/nf-core/modules/fastqc/meta.yml @@ -1,52 +1,52 @@ name: fastqc description: Run FastQC on sequenced reads keywords: - - quality control - - qc - - adapters - - fastq + - quality control + - qc + - adapters + - fastq tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ['GPL-2.0-only'] + - fastqc: + description: | + FastQC gives general quality metrics about your reads. + It provides information about the quality score distribution + across your reads, the per base sequence content (%A/C/G/T). + You get information about adapter contamination and other + overrepresented sequences. + homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ + licence: ["GPL-2.0-only"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - html: + type: file + description: FastQC report + pattern: "*_{fastqc.html}" + - zip: + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf index 3dceb162..1264aac1 100644 --- a/modules/nf-core/modules/multiqc/main.nf +++ b/modules/nf-core/modules/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_medium' - conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null) + conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }" input: path multiqc_files @@ -15,6 +15,9 @@ process MULTIQC { path "*_plots" , optional:true, emit: plots path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' """ diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/modules/multiqc/meta.yml index 63c75a45..6fa891ef 100644 --- a/modules/nf-core/modules/multiqc/meta.yml +++ b/modules/nf-core/modules/multiqc/meta.yml @@ -1,40 +1,40 @@ name: MultiQC description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - - QC - - bioinformatics tools - - Beautiful stand-alone HTML report + - QC + - bioinformatics tools + - Beautiful stand-alone HTML report tools: - - multiqc: - description: | - MultiQC searches a given directory for analysis logs and compiles a HTML report. - It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - homepage: https://multiqc.info/ - documentation: https://multiqc.info/docs/ - licence: ['GPL-3.0-or-later'] + - multiqc: + description: | + MultiQC searches a given directory for analysis logs and compiles a HTML report. + It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + homepage: https://multiqc.info/ + documentation: https://multiqc.info/docs/ + licence: ["GPL-3.0-or-later"] input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC output: - - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - type: dir - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - report: + type: file + description: MultiQC report file + pattern: "multiqc_report.html" + - data: + type: dir + description: MultiQC data dir + pattern: "multiqc_data" + - plots: + type: file + description: Plots created by MultiQC + pattern: "*_data" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@abhi18av" - - "@bunop" - - "@drpatelh" + - "@abhi18av" + - "@bunop" + - "@drpatelh" diff --git a/nextflow_schema.json b/nextflow_schema.json index 0d4d7f78..f39b745e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,10 +10,7 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": [ - "input", - "outdir" - ], + "required": ["input", "outdir"], "properties": { "input": { "type": "string", @@ -185,14 +182,7 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": [ - "symlink", - "rellink", - "link", - "copy", - "copyNoFollow", - "move" - ], + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "hidden": true }, "email_on_fail": { diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 47913e2a..c9d60ecf 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -23,7 +23,7 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true) +ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() /* From ecf6fbb652459ab45d02f7cb7d7579088f8199f0 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 24 Mar 2022 11:33:30 +0000 Subject: [PATCH 04/21] Template update for nf-core/tools version 2.3.2 --- .github/PULL_REQUEST_TEMPLATE.md | 1 - .github/workflows/awsfulltest.yml | 2 -- .github/workflows/awstest.yml | 2 -- .gitpod.yml | 2 +- CHANGELOG.md | 2 -- 5 files changed, 1 insertion(+), 8 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index d4f73bf9..47ed4c45 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -10,7 +10,6 @@ Remember that PRs should be made against the dev branch, unless you're preparing Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md) --> - ## PR checklist diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 4e7752bc..282d8ab7 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -22,8 +22,6 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - pipeline: ${{ github.repository }} - revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bacass/work-${{ github.sha }} parameters: | { diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index e04a4be1..9d0b0477 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -17,8 +17,6 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - pipeline: ${{ github.repository }} - revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bacass/work-${{ github.sha }} parameters: | { diff --git a/.gitpod.yml b/.gitpod.yml index c452ee93..85d95ecc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,7 +4,7 @@ vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files # - cssho.vscode-svgviewer # SVG viewer - - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code + - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar diff --git a/CHANGELOG.md b/CHANGELOG.md index c5db3c7f..3afacd9b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,8 +11,6 @@ Initial release of nf-core/bacass, created with the [nf-core](https://nf-co.re/) ### `Fixed` -- Clarified conda usage and added an installation tutorial for Singularity since the one on Syllabs' website uses an outdate version of GO Compiler - ### `Dependencies` ### `Deprecated` From 270849a803d3aff717a04a9c67e3a523941e6dc4 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 16 May 2022 10:16:01 +0000 Subject: [PATCH 05/21] Template update for nf-core/tools version 2.4 --- .github/workflows/awsfulltest.yml | 3 - .github/workflows/awstest.yml | 3 - .github/workflows/branch.yml | 3 +- .github/workflows/ci.yml | 2 - .github/workflows/fix-linting.yml | 55 ++++++++++ .github/workflows/linting.yml | 4 +- .github/workflows/linting_comment.yml | 1 - .prettierignore | 9 ++ README.md | 25 ++--- assets/email_template.html | 142 ++++++++------------------ bin/check_samplesheet.py | 16 ++- nextflow.config | 2 +- 12 files changed, 135 insertions(+), 130 deletions(-) create mode 100644 .github/workflows/fix-linting.yml create mode 100644 .prettierignore diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 282d8ab7..9e5c20c8 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -28,6 +28,3 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-${{ github.sha }}" } profiles: test_full,aws_tower - nextflow_config: | - process.errorStrategy = 'retry' - process.maxRetries = 3 diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 9d0b0477..22683509 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -23,6 +23,3 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-test-${{ github.sha }}" } profiles: test,aws_tower - nextflow_config: | - process.errorStrategy = 'retry' - process.maxRetries = 3 diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 5ae4f83e..aaaa127d 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,7 +13,7 @@ jobs: - name: Check PRs if: github.repository == 'nf-core/bacass' run: | - "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/bacass ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]" + { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/bacass ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets @@ -42,4 +42,3 @@ jobs: Thanks again for your contribution! repo-token: ${{ secrets.GITHUB_TOKEN }} allow-repeats: false -# diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c4e0a928..832e83dc 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -48,5 +48,3 @@ jobs: # Remember that you can parallelise this by using strategy.matrix run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results - -# diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml new file mode 100644 index 00000000..05f28000 --- /dev/null +++ b/.github/workflows/fix-linting.yml @@ -0,0 +1,55 @@ +name: Fix linting from a comment +on: + issue_comment: + types: [created] + +jobs: + deploy: + # Only run if comment is on a PR with the main repo, and if it contains the magic keywords + if: > + contains(github.event.comment.html_url, '/pull/') && + contains(github.event.comment.body, '@nf-core-bot fix linting') && + github.repository == 'nf-core/bacass' + runs-on: ubuntu-latest + steps: + # Use the @nf-core-bot token to check out so we can push later + - uses: actions/checkout@v3 + with: + token: ${{ secrets.nf_core_bot_auth_token }} + + # Action runs on the issue comment, so we don't get the PR by default + # Use the gh cli to check out the PR + - name: Checkout Pull Request + run: gh pr checkout ${{ github.event.issue.number }} + env: + GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} + + - uses: actions/setup-node@v2 + + - name: Install Prettier + run: npm install -g prettier @prettier/plugin-php + + # Check that we actually need to fix something + - name: Run 'prettier --check' + id: prettier_status + run: | + if prettier --check ${GITHUB_WORKSPACE}; then + echo "::set-output name=result::pass" + else + echo "::set-output name=result::fail" + fi + + - name: Run 'prettier --write' + if: steps.prettier_status.outputs.result == 'fail' + run: prettier --write ${GITHUB_WORKSPACE} + + - name: Commit & push changes + if: steps.prettier_status.outputs.result == 'fail' + run: | + git config user.email "core@nf-co.re" + git config user.name "nf-core-bot" + git config push.default upstream + git add . + git status + git commit -m "[automated] Fix linting with Prettier" + git push diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index e9cf5de3..77358dee 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -48,7 +48,7 @@ jobs: wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - - uses: actions/setup-python@v1 + - uses: actions/setup-python@v3 with: python-version: "3.6" architecture: "x64" @@ -78,5 +78,3 @@ jobs: lint_log.txt lint_results.md PR_number.txt - -# diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 91c487a1..04758f61 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -26,4 +26,3 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} path: linting-logs/lint_results.md -# diff --git a/.prettierignore b/.prettierignore new file mode 100644 index 00000000..d0e7ae58 --- /dev/null +++ b/.prettierignore @@ -0,0 +1,9 @@ +email_template.html +.nextflow* +work/ +data/ +results/ +.DS_Store +testing/ +testing* +*.pyc diff --git a/README.md b/README.md index eccd8cf9..c066af2d 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,19 @@ -# ![nf-core/bacass](docs/images/nf-core/bacass_logo_light.png#gh-light-mode-only) ![nf-core/bacass](docs/images/nf-core/bacass_logo_dark.png#gh-dark-mode-only) +# ![nf-core/bacass](docs/images/nf-core-bacass_logo_light.png#gh-light-mode-only) ![nf-core/bacass](docs/images/nf-core-bacass_logo_dark.png#gh-dark-mode-only) [![GitHub Actions CI Status](https://github.com/nf-core/bacass/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/bacass/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/bacass/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/bacass/actions?query=workflow%3A%22nf-core+linting%22) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/bacass/results) -[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) - -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/) -[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) -[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) -[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) - -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23bacass-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/bacass) -[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core) -[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/bacass/results) +[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8)](https://doi.org/10.5281/zenodo.XXXXXXX) + +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/) +[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/) +[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/) +[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/) +[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/bacass) + +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23bacass-4A154B?logo=slack)](https://nfcore.slack.com/channels/bacass) +[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core) +[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction diff --git a/assets/email_template.html b/assets/email_template.html index 49c7405c..ebf8e7a3 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -1,111 +1,53 @@ - - - - + + + + - - - nf-core/bacass Pipeline Report - - -
- + + nf-core/bacass Pipeline Report + + +
-

nf-core/bacass v${version}

-

Run Name: $runName

+ - <% if (!success){ out << """ -
-

nf-core/bacass execution completed unsuccessfully!

+

nf-core/bacass v${version}

+

Run Name: $runName

+ +<% if (!success){ + out << """ +
+

nf-core/bacass execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: $exitStatus.

The full error message was:

- 
${errorReport}
-
- """ } else { out << """ -
+ 
${errorReport}
+
+ """ +} else { + out << """ +
nf-core/bacass execution completed successfully! -
- """ } %> +
+ """ +} +%> -

The workflow was completed at $dateComplete (duration: $duration)

-

The command used to launch the workflow was as follows:

- 
-$commandLine
+

The workflow was completed at $dateComplete (duration: $duration)

+

The command used to launch the workflow was as follows:

+
$commandLine
-

Pipeline Configuration:

- - - <% out << summary.collect{ k,v -> " - - - - - " }.join("\n") %> - -
- $k - - 
$v
-
+

Pipeline Configuration:

+ + + <% out << summary.collect{ k,v -> "" }.join("\n") %> + +
$k
$v
-

nf-core/bacass

-

https://github.com/nf-core/bacass

-
- +

nf-core/bacass

+

https://github.com/nf-core/bacass

+ +
+ + diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 5473b624..3652c63c 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -98,7 +98,7 @@ def _validate_pair(self, row): if row[self._first_col] and row[self._second_col]: row[self._single_col] = False assert ( - Path(row[self._first_col]).suffixes == Path(row[self._second_col]).suffixes + Path(row[self._first_col]).suffixes[-2:] == Path(row[self._second_col]).suffixes[-2:] ), "FASTQ pairs must have the same file extensions." else: row[self._single_col] = True @@ -129,6 +129,16 @@ def validate_unique_samples(self): row[self._sample_col] = f"{sample}_T{seen[sample]}" +def read_head(handle, num_lines=10): + """Read the specified number of lines from the current position in the file.""" + lines = [] + for idx, line in enumerate(handle): + if idx == num_lines: + break + lines.append(line) + return "".join(lines) + + def sniff_format(handle): """ Detect the tabular format. @@ -144,13 +154,13 @@ def sniff_format(handle): https://docs.python.org/3/glossary.html#term-text-file """ - peek = handle.read(2048) + peek = read_head(handle) + handle.seek(0) sniffer = csv.Sniffer() if not sniffer.has_header(peek): logger.critical(f"The given sample sheet does not appear to contain a header.") sys.exit(1) dialect = sniffer.sniff(peek) - handle.seek(0) return dialect diff --git a/nextflow.config b/nextflow.config index dccfc2ba..1d01e4e8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -159,7 +159,7 @@ trace { } dag { enabled = true - file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg" + file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" } manifest { From 2c8a2a72a349eab41d037a9a5262c9eeb1dc4898 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 30 Aug 2022 13:31:14 +0000 Subject: [PATCH 06/21] Template update for nf-core/tools version 2.5 --- .editorconfig | 2 +- .github/PULL_REQUEST_TEMPLATE.md | 3 +- .github/workflows/ci.yml | 23 ++------ .github/workflows/linting.yml | 38 +++++++++++-- CITATION.cff | 56 +++++++++++++++++++ README.md | 21 +++---- assets/email_template.txt | 1 - bin/check_samplesheet.py | 41 +++++++------- conf/base.config | 5 ++ docs/usage.md | 12 ++-- lib/WorkflowBacass.groovy | 5 +- lib/WorkflowMain.groovy | 9 ++- main.nf | 2 +- modules.json | 22 +++++--- .../templates/dumpsoftwareversions.py | 14 +++-- nextflow.config | 21 ++++++- 16 files changed, 184 insertions(+), 91 deletions(-) create mode 100644 CITATION.cff diff --git a/.editorconfig b/.editorconfig index b6b31907..b78de6e6 100644 --- a/.editorconfig +++ b/.editorconfig @@ -8,7 +8,7 @@ trim_trailing_whitespace = true indent_size = 4 indent_style = space -[*.{md,yml,yaml,html,css,scss,js}] +[*.{md,yml,yaml,html,css,scss,js,cff}] indent_size = 2 # These files are edited and tested upstream in nf-core/modules diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 47ed4c45..0c7eab4a 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/baca - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md) - - [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 832e83dc..a880e241 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -10,7 +10,6 @@ on: env: NXF_ANSI_LOG: false - CAPSULE_LOG: none jobs: test: @@ -20,27 +19,17 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - # Nextflow versions - include: - # Test pipeline minimum Nextflow version - - NXF_VER: "21.10.3" - NXF_EDGE: "" - # Test latest edge release of Nextflow - - NXF_VER: "" - NXF_EDGE: "1" + NXF_VER: + - "21.10.3" + - "latest-everything" steps: - name: Check out pipeline code uses: actions/checkout@v2 - name: Install Nextflow - env: - NXF_VER: ${{ matrix.NXF_VER }} - # Uncomment only if the edge release is more recent than the latest stable release - # See https://github.com/nextflow-io/nextflow/issues/2467 - # NXF_EDGE: ${{ matrix.NXF_EDGE }} - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ + uses: nf-core/setup-nextflow@v1 + with: + version: "${{ matrix.NXF_VER }}" - name: Run pipeline with test data # TODO nf-core: You can customise CI pipeline run tests as required diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 77358dee..8a5ce69b 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -35,6 +35,36 @@ jobs: - name: Run Prettier --check run: prettier --check ${GITHUB_WORKSPACE} + PythonBlack: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + + - name: Check code lints with Black + uses: psf/black@stable + + # If the above check failed, post a comment on the PR explaining the failure + - name: Post PR comment + if: failure() + uses: mshick/add-pr-comment@v1 + with: + message: | + ## Python linting (`black`) is failing + + To keep the code consistent with lots of contributors, we run automated code consistency checks. + To fix this CI test, please run: + + * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black` + * Fix formatting errors in your pipeline: `black .` + + Once you push these changes the test should pass, and you can hide this comment :+1: + + We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! + + Thanks again for your contribution! + repo-token: ${{ secrets.GITHUB_TOKEN }} + allow-repeats: false + nf-core: runs-on: ubuntu-latest steps: @@ -42,15 +72,11 @@ jobs: uses: actions/checkout@v2 - name: Install Nextflow - env: - CAPSULE_LOG: none - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@v3 with: - python-version: "3.6" + python-version: "3.7" architecture: "x64" - name: Install dependencies diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..4533e2f2 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,56 @@ +cff-version: 1.2.0 +message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication" +authors: + - family-names: Ewels + given-names: Philip + - family-names: Peltzer + given-names: Alexander + - family-names: Fillinger + given-names: Sven + - family-names: Patel + given-names: Harshil + - family-names: Alneberg + given-names: Johannes + - family-names: Wilm + given-names: Andreas + - family-names: Ulysse Garcia + given-names: Maxime + - family-names: Di Tommaso + given-names: Paolo + - family-names: Nahnsen + given-names: Sven +title: "The nf-core framework for community-curated bioinformatics pipelines." +version: 2.4.1 +doi: 10.1038/s41587-020-0439-x +date-released: 2022-05-16 +url: https://github.com/nf-core/tools +prefered-citation: + type: article + authors: + - family-names: Ewels + given-names: Philip + - family-names: Peltzer + given-names: Alexander + - family-names: Fillinger + given-names: Sven + - family-names: Patel + given-names: Harshil + - family-names: Alneberg + given-names: Johannes + - family-names: Wilm + given-names: Andreas + - family-names: Ulysse Garcia + given-names: Maxime + - family-names: Di Tommaso + given-names: Paolo + - family-names: Nahnsen + given-names: Sven + doi: 10.1038/s41587-020-0439-x + journal: nature biotechnology + start: 276 + end: 278 + title: "The nf-core framework for community-curated bioinformatics pipelines." + issue: 3 + volume: 38 + year: 2020 + url: https://dx.doi.org/10.1038/s41587-020-0439-x diff --git a/README.md b/README.md index c066af2d..ddd4f49a 100644 --- a/README.md +++ b/README.md @@ -1,19 +1,14 @@ # ![nf-core/bacass](docs/images/nf-core-bacass_logo_light.png#gh-light-mode-only) ![nf-core/bacass](docs/images/nf-core-bacass_logo_dark.png#gh-dark-mode-only) -[![GitHub Actions CI Status](https://github.com/nf-core/bacass/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/bacass/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/bacass/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/bacass/actions?query=workflow%3A%22nf-core+linting%22) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/bacass/results) -[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/bacass/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/) -[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/) -[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/) -[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/) +[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) +[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) +[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/bacass) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23bacass-4A154B?logo=slack)](https://nfcore.slack.com/channels/bacass) -[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core) -[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23bacass-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/bacass)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction @@ -25,7 +20,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool -On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/bacass/results). +On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/bacass/results). ## Pipeline summary @@ -42,7 +37,7 @@ On release, automated continuous integration tests run the pipeline on a full-si 3. Download the pipeline and test it on a minimal dataset with a single command: - ```console + ```bash nextflow run nf-core/bacass -profile test,YOURPROFILE --outdir ``` @@ -57,7 +52,7 @@ On release, automated continuous integration tests run the pipeline on a full-si - ```console + ```bash nextflow run nf-core/bacass --input samplesheet.csv --outdir --genome GRCh37 -profile ``` diff --git a/assets/email_template.txt b/assets/email_template.txt index ae71982d..6b645199 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -6,7 +6,6 @@ `._,._,' nf-core/bacass v${version} ---------------------------------------------------- - Run Name: $runName <% if (success){ diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 3652c63c..9a8b8962 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -11,7 +11,6 @@ from collections import Counter from pathlib import Path - logger = logging.getLogger() @@ -79,13 +78,15 @@ def validate_and_transform(self, row): def _validate_sample(self, row): """Assert that the sample name exists and convert spaces to underscores.""" - assert len(row[self._sample_col]) > 0, "Sample input is required." + if len(row[self._sample_col]) <= 0: + raise AssertionError("Sample input is required.") # Sanitize samples slightly. row[self._sample_col] = row[self._sample_col].replace(" ", "_") def _validate_first(self, row): """Assert that the first FASTQ entry is non-empty and has the right format.""" - assert len(row[self._first_col]) > 0, "At least the first FASTQ file is required." + if len(row[self._first_col]) <= 0: + raise AssertionError("At least the first FASTQ file is required.") self._validate_fastq_format(row[self._first_col]) def _validate_second(self, row): @@ -97,36 +98,34 @@ def _validate_pair(self, row): """Assert that read pairs have the same file extension. Report pair status.""" if row[self._first_col] and row[self._second_col]: row[self._single_col] = False - assert ( - Path(row[self._first_col]).suffixes[-2:] == Path(row[self._second_col]).suffixes[-2:] - ), "FASTQ pairs must have the same file extensions." + if Path(row[self._first_col]).suffixes[-2:] != Path(row[self._second_col]).suffixes[-2:]: + raise AssertionError("FASTQ pairs must have the same file extensions.") else: row[self._single_col] = True def _validate_fastq_format(self, filename): """Assert that a given filename has one of the expected FASTQ extensions.""" - assert any(filename.endswith(extension) for extension in self.VALID_FORMATS), ( - f"The FASTQ file has an unrecognized extension: {filename}\n" - f"It should be one of: {', '.join(self.VALID_FORMATS)}" - ) + if not any(filename.endswith(extension) for extension in self.VALID_FORMATS): + raise AssertionError( + f"The FASTQ file has an unrecognized extension: {filename}\n" + f"It should be one of: {', '.join(self.VALID_FORMATS)}" + ) def validate_unique_samples(self): """ Assert that the combination of sample name and FASTQ filename is unique. - In addition to the validation, also rename the sample if more than one sample, - FASTQ file combination exists. + In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the + number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment. """ - assert len(self._seen) == len(self.modified), "The pair of sample name and FASTQ must be unique." - if len({pair[0] for pair in self._seen}) < len(self._seen): - counts = Counter(pair[0] for pair in self._seen) - seen = Counter() - for row in self.modified: - sample = row[self._sample_col] - seen[sample] += 1 - if counts[sample] > 1: - row[self._sample_col] = f"{sample}_T{seen[sample]}" + if len(self._seen) != len(self.modified): + raise AssertionError("The pair of sample name and FASTQ must be unique.") + seen = Counter() + for row in self.modified: + sample = row[self._sample_col] + seen[sample] += 1 + row[self._sample_col] = f"{sample}_T{seen[sample]}" def read_head(handle, num_lines=10): diff --git a/conf/base.config b/conf/base.config index fb20f020..afca6212 100644 --- a/conf/base.config +++ b/conf/base.config @@ -26,6 +26,11 @@ process { // adding in your local modules too. // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors + withLabel:process_single { + cpus = { check_max( 1 , 'cpus' ) } + memory = { check_max( 6.GB * task.attempt, 'memory' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } + } withLabel:process_low { cpus = { check_max( 2 * task.attempt, 'cpus' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) } diff --git a/docs/usage.md b/docs/usage.md index a3982540..4ae024f7 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -12,7 +12,7 @@ You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below. -```console +```bash --input '[path to samplesheet file]' ``` @@ -56,7 +56,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: -```console +```bash nextflow run nf-core/bacass --input samplesheet.csv --outdir --genome GRCh37 -profile docker ``` @@ -64,9 +64,9 @@ This will launch the pipeline with the `docker` configuration profile. See below Note that the pipeline will create the following files in your working directory: -```console +```bash work # Directory containing the nextflow working files - # Finished results in specified location (defined with --outdir) + # Finished results in specified location (defined with --outdir) .nextflow_log # Log file from Nextflow # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` @@ -75,7 +75,7 @@ work # Directory containing the nextflow working files When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: -```console +```bash nextflow pull nf-core/bacass ``` @@ -251,6 +251,6 @@ Some HPC setups also allow you to run nextflow within a cluster job submitted yo In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`): -```console +```bash NXF_OPTS='-Xms1g -Xmx4g' ``` diff --git a/lib/WorkflowBacass.groovy b/lib/WorkflowBacass.groovy index aa100683..8d85cef7 100755 --- a/lib/WorkflowBacass.groovy +++ b/lib/WorkflowBacass.groovy @@ -10,6 +10,7 @@ class WorkflowBacass { public static void initialise(params, log) { genomeExistsError(params, log) + if (!params.fasta) { log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." System.exit(1) @@ -41,9 +42,7 @@ class WorkflowBacass { yaml_file_text += "data: |\n" yaml_file_text += "${summary_section}" return yaml_file_text - } - - // + }// // Exit pipeline if incorrect --genome key provided // private static void genomeExistsError(params, log) { diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 2db15275..8379896f 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -59,6 +59,7 @@ class WorkflowMain { } // Print parameter summary log to screen + log.info paramsSummaryLog(workflow, params, log) // Check that a -profile or Nextflow config has been provided to run the pipeline @@ -78,17 +79,15 @@ class WorkflowMain { System.exit(1) } } - // // Get attribute from genome config file e.g. fasta // - public static String getGenomeAttribute(params, attribute) { - def val = '' + public static Object getGenomeAttribute(params, attribute) { if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { if (params.genomes[ params.genome ].containsKey(attribute)) { - val = params.genomes[ params.genome ][ attribute ] + return params.genomes[ params.genome ][ attribute ] } } - return val + return null } } diff --git a/main.nf b/main.nf index 6b776dd9..484504a7 100644 --- a/main.nf +++ b/main.nf @@ -4,7 +4,7 @@ nf-core/bacass ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/bacass - Website: https://nf-co.re/bacass +Website: https://nf-co.re/bacass Slack : https://nfcore.slack.com/channels/bacass ---------------------------------------------------------------------------------------- */ diff --git a/modules.json b/modules.json index 91697355..15e1238a 100644 --- a/modules.json +++ b/modules.json @@ -3,14 +3,20 @@ "homePage": "https://github.com/nf-core/bacass", "repos": { "nf-core/modules": { - "custom/dumpsoftwareversions": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" - }, - "fastqc": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" - }, - "multiqc": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" + "git_url": "https://github.com/nf-core/modules.git", + "modules": { + "custom/dumpsoftwareversions": { + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", + "branch": "master" + }, + "fastqc": { + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", + "branch": "master" + }, + "multiqc": { + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", + "branch": "master" + } } } } diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index d1390392..787bdb7b 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -1,9 +1,10 @@ #!/usr/bin/env python -import yaml import platform from textwrap import dedent +import yaml + def _make_versions_html(versions): html = [ @@ -58,11 +59,12 @@ def _make_versions_html(versions): for process, process_versions in versions_by_process.items(): module = process.split(":")[-1] try: - assert versions_by_module[module] == process_versions, ( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) + if versions_by_module[module] != process_versions: + raise AssertionError( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) except KeyError: versions_by_module[module] = process_versions diff --git a/nextflow.config b/nextflow.config index 1d01e4e8..6d6bf3b8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -13,11 +13,11 @@ params { // Input options input = null + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false - // MultiQC options multiqc_config = null multiqc_title = null @@ -37,6 +37,7 @@ params { schema_ignore_params = 'genomes' enable_conda = false + // Config options custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" @@ -45,6 +46,7 @@ params { config_profile_url = null config_profile_name = null + // Max resource options // Defaults only, expecting to be overwritten max_memory = '128.GB' @@ -72,6 +74,7 @@ try { // } + profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { @@ -82,6 +85,15 @@ profiles { shifter.enabled = false charliecloud.enabled = false } + mamba { + params.enable_conda = true + conda.useMamba = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } docker { docker.enabled = true docker.userEmulation = true @@ -119,10 +131,16 @@ profiles { podman.enabled = false shifter.enabled = false } + gitpod { + executor.name = 'local' + executor.cpus = 16 + executor.memory = 60.GB + } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } + // Load igenomes.config if required if (!params.igenomes_ignore) { includeConfig 'conf/igenomes.config' @@ -130,6 +148,7 @@ if (!params.igenomes_ignore) { params.genomes = [:] } + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. From 8d72268a8221886ae0dcc841de2f74b9bca4b51a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 1 Sep 2022 13:23:23 +0000 Subject: [PATCH 07/21] Template update for nf-core/tools version 2.5.1 --- bin/check_samplesheet.py | 9 ++++++--- pyproject.toml | 10 ++++++++++ 2 files changed, 16 insertions(+), 3 deletions(-) create mode 100644 pyproject.toml diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 9a8b8962..11b15572 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -98,7 +98,9 @@ def _validate_pair(self, row): """Assert that read pairs have the same file extension. Report pair status.""" if row[self._first_col] and row[self._second_col]: row[self._single_col] = False - if Path(row[self._first_col]).suffixes[-2:] != Path(row[self._second_col]).suffixes[-2:]: + first_col_suffix = Path(row[self._first_col]).suffixes[-2:] + second_col_suffix = Path(row[self._second_col]).suffixes[-2:] + if first_col_suffix != second_col_suffix: raise AssertionError("FASTQ pairs must have the same file extensions.") else: row[self._single_col] = True @@ -157,7 +159,7 @@ def sniff_format(handle): handle.seek(0) sniffer = csv.Sniffer() if not sniffer.has_header(peek): - logger.critical(f"The given sample sheet does not appear to contain a header.") + logger.critical("The given sample sheet does not appear to contain a header.") sys.exit(1) dialect = sniffer.sniff(peek) return dialect @@ -195,7 +197,8 @@ def check_samplesheet(file_in, file_out): reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) # Validate the existence of the expected header columns. if not required_columns.issubset(reader.fieldnames): - logger.critical(f"The sample sheet **must** contain the column headers: {', '.join(required_columns)}.") + req_cols = ", ".join(required_columns) + logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.") sys.exit(1) # Validate each row. checker = RowChecker() diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..0d62beb6 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,10 @@ +# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black. +# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. +[tool.black] +line-length = 120 +target_version = ["py37", "py38", "py39", "py310"] + +[tool.isort] +profile = "black" +known_first_party = ["nf_core"] +multi_line_output = 3 From 152aed32434ed606b3ea3c030df7a1102abf25c3 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 4 Oct 2022 21:53:01 +0000 Subject: [PATCH 08/21] Template update for nf-core/tools version 2.6 --- .github/workflows/awsfulltest.yml | 4 ++ .github/workflows/awstest.yml | 4 ++ .prettierignore | 1 + CITATION.cff | 8 +-- assets/adaptivecard.json | 67 +++++++++++++++++++ assets/methods_description_template.yml | 25 +++++++ assets/multiqc_config.yml | 6 +- docs/usage.md | 8 +++ lib/NfcoreTemplate.groovy | 55 +++++++++++++++ lib/Utils.groovy | 21 ++++-- lib/WorkflowBacass.groovy | 19 ++++++ main.nf | 3 +- modules.json | 27 ++++---- .../custom/dumpsoftwareversions/main.nf | 8 +-- .../custom/dumpsoftwareversions/meta.yml | 0 .../templates/dumpsoftwareversions.py | 0 modules/nf-core/{modules => }/fastqc/main.nf | 12 ++++ modules/nf-core/{modules => }/fastqc/meta.yml | 0 modules/nf-core/modules/multiqc/main.nf | 31 --------- modules/nf-core/multiqc/main.nf | 53 +++++++++++++++ .../nf-core/{modules => }/multiqc/meta.yml | 15 +++++ nextflow.config | 5 +- nextflow_schema.json | 18 +++++ workflows/bacass.nf | 26 ++++--- 24 files changed, 345 insertions(+), 71 deletions(-) create mode 100644 assets/adaptivecard.json create mode 100644 assets/methods_description_template.yml mode change 100755 => 100644 lib/Utils.groovy rename modules/nf-core/{modules => }/custom/dumpsoftwareversions/main.nf (79%) rename modules/nf-core/{modules => }/custom/dumpsoftwareversions/meta.yml (100%) rename modules/nf-core/{modules => }/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py (100%) rename modules/nf-core/{modules => }/fastqc/main.nf (85%) rename modules/nf-core/{modules => }/fastqc/meta.yml (100%) delete mode 100644 modules/nf-core/modules/multiqc/main.nf create mode 100644 modules/nf-core/multiqc/main.nf rename modules/nf-core/{modules => }/multiqc/meta.yml (73%) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 9e5c20c8..0e1f0216 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -28,3 +28,7 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-${{ github.sha }}" } profiles: test_full,aws_tower + - uses: actions/upload-artifact@v3 + with: + name: Tower debug log file + path: tower_action_*.log diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 22683509..5ad2d9b0 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -23,3 +23,7 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-test-${{ github.sha }}" } profiles: test,aws_tower + - uses: actions/upload-artifact@v3 + with: + name: Tower debug log file + path: tower_action_*.log diff --git a/.prettierignore b/.prettierignore index d0e7ae58..eb74a574 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,4 +1,5 @@ email_template.html +adaptivecard.json .nextflow* work/ data/ diff --git a/CITATION.cff b/CITATION.cff index 4533e2f2..017666c0 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -13,8 +13,8 @@ authors: given-names: Johannes - family-names: Wilm given-names: Andreas - - family-names: Ulysse Garcia - given-names: Maxime + - family-names: Garcia + given-names: Maxime Ulysse - family-names: Di Tommaso given-names: Paolo - family-names: Nahnsen @@ -39,8 +39,8 @@ prefered-citation: given-names: Johannes - family-names: Wilm given-names: Andreas - - family-names: Ulysse Garcia - given-names: Maxime + - family-names: Garcia + given-names: Maxime Ulysse - family-names: Di Tommaso given-names: Paolo - family-names: Nahnsen diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json new file mode 100644 index 00000000..52b0afd4 --- /dev/null +++ b/assets/adaptivecard.json @@ -0,0 +1,67 @@ +{ + "type": "message", + "attachments": [ + { + "contentType": "application/vnd.microsoft.card.adaptive", + "contentUrl": null, + "content": { + "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", + "msteams": { + "width": "Full" + }, + "type": "AdaptiveCard", + "version": "1.2", + "body": [ + { + "type": "TextBlock", + "size": "Large", + "weight": "Bolder", + "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", + "text": "nf-core/bacass v${version} - ${runName}", + "wrap": true + }, + { + "type": "TextBlock", + "spacing": "None", + "text": "Completed at ${dateComplete} (duration: ${duration})", + "isSubtle": true, + "wrap": true + }, + { + "type": "TextBlock", + "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>", + "wrap": true + }, + { + "type": "TextBlock", + "text": "The command used to launch the workflow was as follows:", + "wrap": true + }, + { + "type": "TextBlock", + "text": "${commandLine}", + "isSubtle": true, + "wrap": true + } + ], + "actions": [ + { + "type": "Action.ShowCard", + "title": "Pipeline Configuration", + "card": { + "type": "AdaptiveCard", + "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", + "body": [ + { + "type": "FactSet", + "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %> + ] + } + ] + } + } + ] + } + } + ] +} diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml new file mode 100644 index 00000000..a19f3abb --- /dev/null +++ b/assets/methods_description_template.yml @@ -0,0 +1,25 @@ +id: "nf-core-bacass-methods-description" +description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." +section_name: "nf-core/bacass Methods Description" +section_href: "https://github.com/nf-core/bacass" +plot_type: "html" +## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline +## You inject any metadata in the Nextflow '${workflow}' object +data: | +

Methods

+

Data was processed using nf-core/bacass v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

+

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

+ 
${workflow.commandLine}
+

References

+
    +
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
    • +
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
    • +
+
+
Notes:
+
    + ${nodoi_text} +
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
    • +
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
    • +
+
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index c16e95ab..5217b52e 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,9 +3,11 @@ report_comment: > analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: - software_versions: + "nf-core-bacass-methods-description": order: -1000 - "nf-core-bacass-summary": + software_versions: order: -1001 + "nf-core-bacass-summary": + order: -1002 export_plots: true diff --git a/docs/usage.md b/docs/usage.md index 4ae024f7..dd339d43 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -237,6 +237,14 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). +## Azure Resource Requests + +To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. +We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. + +Note that the choice of VM size depends on your quota and the overall workload during the analysis. +For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). + ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 2fc0a9b9..27feb009 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -145,6 +145,61 @@ class NfcoreTemplate { output_tf.withWriter { w -> w << email_txt } } + // + // Construct and send adaptive card + // https://adaptivecards.io + // + public static void adaptivecard(workflow, params, summary_params, projectDir, log) { + def hook_url = params.hook_url + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = workflow.manifest.version + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + def hf = new File("$projectDir/assets/adaptivecard.json") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection(); + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); + } + } + // // Print pipeline summary on completion // diff --git a/lib/Utils.groovy b/lib/Utils.groovy old mode 100755 new mode 100644 index 28567bd7..8d030f4e --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -21,19 +21,26 @@ class Utils { } // Check that all channels are present - def required_channels = ['conda-forge', 'bioconda', 'defaults'] - def conda_check_failed = !required_channels.every { ch -> ch in channels } + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda')) - conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults')) + def channel_priority_violation = false + def n = required_channels_in_order.size() + for (int i = 0; i < n - 1; i++) { + channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + } - if (conda_check_failed) { + if (channels_missing | channel_priority_violation) { log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" + - " NB: The order of the channels matters!\n" + + " Please refer to https://bioconda.github.io/\n" + + " The observed channel order is \n" + + " ${channels}\n" + + " but the following channel order is required:\n" + + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } } diff --git a/lib/WorkflowBacass.groovy b/lib/WorkflowBacass.groovy index 8d85cef7..c8f87332 100755 --- a/lib/WorkflowBacass.groovy +++ b/lib/WorkflowBacass.groovy @@ -2,6 +2,8 @@ // This file holds several functions specific to the workflow/bacass.nf in the nf-core/bacass pipeline // +import groovy.text.SimpleTemplateEngine + class WorkflowBacass { // @@ -42,6 +44,23 @@ class WorkflowBacass { yaml_file_text += "data: |\n" yaml_file_text += "${summary_section}" return yaml_file_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = run_workflow.toMap() + meta["manifest_map"] = run_workflow.manifest.toMap() + + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + + def methods_text = mqc_methods_yaml.text + + def engine = new SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html }// // Exit pipeline if incorrect --genome key provided // diff --git a/main.nf b/main.nf index 484504a7..3e800210 100644 --- a/main.nf +++ b/main.nf @@ -4,7 +4,8 @@ nf-core/bacass ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/bacass -Website: https://nf-co.re/bacass + + Website: https://nf-co.re/bacass Slack : https://nfcore.slack.com/channels/bacass ---------------------------------------------------------------------------------------- */ diff --git a/modules.json b/modules.json index 15e1238a..80d8edb7 100644 --- a/modules.json +++ b/modules.json @@ -2,20 +2,21 @@ "name": "nf-core/bacass", "homePage": "https://github.com/nf-core/bacass", "repos": { - "nf-core/modules": { - "git_url": "https://github.com/nf-core/modules.git", + "https://github.com/nf-core/modules.git": { "modules": { - "custom/dumpsoftwareversions": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", - "branch": "master" - }, - "fastqc": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", - "branch": "master" - }, - "multiqc": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", - "branch": "master" + "nf-core": { + "custom/dumpsoftwareversions": { + "branch": "master", + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + }, + "fastqc": { + "branch": "master", + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + }, + "multiqc": { + "branch": "master", + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + } } } } diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf similarity index 79% rename from modules/nf-core/modules/custom/dumpsoftwareversions/main.nf rename to modules/nf-core/custom/dumpsoftwareversions/main.nf index 327d5100..cebb6e05 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -1,11 +1,11 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_low' + label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda (params.enable_conda ? "bioconda::multiqc=1.11" : null) + conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml similarity index 100% rename from modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml rename to modules/nf-core/custom/dumpsoftwareversions/meta.yml diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py similarity index 100% rename from modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py rename to modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/fastqc/main.nf similarity index 85% rename from modules/nf-core/modules/fastqc/main.nf rename to modules/nf-core/fastqc/main.nf index ed6b8c50..05730368 100644 --- a/modules/nf-core/modules/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -44,4 +44,16 @@ process FASTQC { END_VERSIONS """ } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.html + touch ${prefix}.zip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ } diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml similarity index 100% rename from modules/nf-core/modules/fastqc/meta.yml rename to modules/nf-core/fastqc/meta.yml diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf deleted file mode 100644 index 1264aac1..00000000 --- a/modules/nf-core/modules/multiqc/main.nf +++ /dev/null @@ -1,31 +0,0 @@ -process MULTIQC { - label 'process_medium' - - conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }" - - input: - path multiqc_files - - output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - """ - multiqc -f $args . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf new file mode 100644 index 00000000..a8159a57 --- /dev/null +++ b/modules/nf-core/multiqc/main.nf @@ -0,0 +1,53 @@ +process MULTIQC { + label 'process_single' + + conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + + input: + path multiqc_files, stageAs: "?/*" + path(multiqc_config) + path(extra_multiqc_config) + path(multiqc_logo) + + output: + path "*multiqc_report.html", emit: report + path "*_data" , emit: data + path "*_plots" , optional:true, emit: plots + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def config = multiqc_config ? "--config $multiqc_config" : '' + def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + """ + multiqc \\ + --force \\ + $args \\ + $config \\ + $extra_config \\ + . + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + """ + + stub: + """ + touch multiqc_data + touch multiqc_plots + touch multiqc_report.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml similarity index 73% rename from modules/nf-core/modules/multiqc/meta.yml rename to modules/nf-core/multiqc/meta.yml index 6fa891ef..ebc29b27 100644 --- a/modules/nf-core/modules/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -12,11 +12,25 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + input: - multiqc_files: type: file description: | List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. + pattern: "*.{yml,yaml}" + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + output: - report: type: file @@ -38,3 +52,4 @@ authors: - "@abhi18av" - "@bunop" - "@drpatelh" + - "@jfy133" diff --git a/nextflow.config b/nextflow.config index 6d6bf3b8..4f42c8c3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -21,7 +21,9 @@ params { // MultiQC options multiqc_config = null multiqc_title = null + multiqc_logo = null max_multiqc_email_size = '25.MB' + multiqc_methods_description = null // Boilerplate options outdir = null @@ -31,6 +33,7 @@ params { email_on_fail = null plaintext_email = false monochrome_logs = false + hook_url = null help = false validate_params = true show_hidden_params = false @@ -74,7 +77,6 @@ try { // } - profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { @@ -189,6 +191,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=21.10.3' version = '2.1.0dev' + doi = '' } // Load modules.config for DSL2 module specific options diff --git a/nextflow_schema.json b/nextflow_schema.json index f39b745e..8538aaac 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -213,12 +213,30 @@ "fa_icon": "fas fa-palette", "hidden": true }, + "hook_url": { + "type": "string", + "description": "Incoming hook URL for messaging service", + "fa_icon": "fas fa-people-group", + "help_text": "Incoming hook URL for messaging service. Currently, only MS Teams is supported.", + "hidden": true + }, "multiqc_config": { "type": "string", "description": "Custom config file to supply to MultiQC.", "fa_icon": "fas fa-cog", "hidden": true }, + "multiqc_logo": { + "type": "string", + "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file", + "fa_icon": "fas fa-image", + "hidden": true + }, + "multiqc_methods_description": { + "type": "string", + "description": "Custom MultiQC yaml file containing HTML including a methods description.", + "fa_icon": "fas fa-cog" + }, "tracedir": { "type": "string", "description": "Directory to keep pipeline Nextflow logs and reports.", diff --git a/workflows/bacass.nf b/workflows/bacass.nf index c9d60ecf..61a125d6 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -23,8 +23,10 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() +ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) +ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() +ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() +ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -46,9 +48,9 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check' // // MODULE: Installed directly from nf-core/modules // -include { FASTQC } from '../modules/nf-core/modules/fastqc/main' -include { MULTIQC } from '../modules/nf-core/modules/multiqc/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -89,15 +91,20 @@ workflow BACASS { workflow_summary = WorkflowBacass.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) + methods_description = WorkflowBacass.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + ch_methods_description = Channel.value(methods_description) + ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config)) - ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) MULTIQC ( - ch_multiqc_files.collect() + ch_multiqc_files.collect(), + ch_multiqc_config.collect().ifEmpty([]), + ch_multiqc_custom_config.collect().ifEmpty([]), + ch_multiqc_logo.collect().ifEmpty([]) ) multiqc_report = MULTIQC.out.report.toList() ch_versions = ch_versions.mix(MULTIQC.out.versions) @@ -114,6 +121,9 @@ workflow.onComplete { NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) } NfcoreTemplate.summary(workflow, params, log) + if (params.hook_url) { + NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log) + } } /* From 3a8ff0b0a3d806c0832235e2ccd12a2214e34b3d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 8 Dec 2022 13:09:25 +0000 Subject: [PATCH 09/21] Template update for nf-core/tools version 2.7.1 --- .devcontainer/devcontainer.json | 27 +++++++++++++ .gitattributes | 1 + .github/CONTRIBUTING.md | 16 ++++++++ .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/workflows/ci.yml | 8 +++- .github/workflows/fix-linting.yml | 6 +-- .github/workflows/linting.yml | 18 +++++---- .github/workflows/linting_comment.yml | 2 +- .prettierignore | 2 + CITATION.cff | 56 --------------------------- README.md | 4 +- assets/slackreport.json | 34 ++++++++++++++++ docs/usage.md | 24 +++++++----- lib/NfcoreSchema.groovy | 1 - lib/NfcoreTemplate.groovy | 41 +++++++++++++++----- lib/WorkflowMain.groovy | 18 ++++++--- modules.json | 9 +++-- modules/local/samplesheet_check.nf | 4 ++ nextflow.config | 12 ++++-- nextflow_schema.json | 8 +++- workflows/bacass.nf | 11 +++--- 21 files changed, 193 insertions(+), 111 deletions(-) create mode 100644 .devcontainer/devcontainer.json delete mode 100644 CITATION.cff create mode 100644 assets/slackreport.json diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 00000000..ea27a584 --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,27 @@ +{ + "name": "nfcore", + "image": "nfcore/gitpod:latest", + "remoteUser": "gitpod", + + // Configure tool-specific properties. + "customizations": { + // Configure properties specific to VS Code. + "vscode": { + // Set *default* container specific settings.json values on container create. + "settings": { + "python.defaultInterpreterPath": "/opt/conda/bin/python", + "python.linting.enabled": true, + "python.linting.pylintEnabled": true, + "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", + "python.formatting.yapfPath": "/opt/conda/bin/yapf", + "python.linting.flake8Path": "/opt/conda/bin/flake8", + "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", + "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", + "python.linting.pylintPath": "/opt/conda/bin/pylint" + }, + + // Add the IDs of extensions you want installed when the container is created. + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] + } + } +} diff --git a/.gitattributes b/.gitattributes index 050bb120..7a2dabc2 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,3 +1,4 @@ *.config linguist-language=nextflow +*.nf.test linguist-language=nextflow modules/nf-core/** linguist-generated subworkflows/nf-core/** linguist-generated diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 60f7799e..33b89e71 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -101,3 +101,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ ### Images and figures For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). + +## GitHub Codespaces + +This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. + +To get started: + +- Open the repo in [Codespaces](https://github.com/nf-core/bacass/codespaces) +- Tools installed + - nf-core + - Nextflow + +Devcontainer specs: + +- [DevContainer config](.devcontainer/devcontainer.json) +- [Dockerfile](.devcontainer/Dockerfile) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 527bcbd4..cb41a232 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -42,7 +42,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 21.10.3)_ + * Nextflow version _(eg. 22.10.1)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a880e241..c91c0fb8 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,6 +11,10 @@ on: env: NXF_ANSI_LOG: false +concurrency: + group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" + cancel-in-progress: true + jobs: test: name: Run pipeline with test data @@ -20,11 +24,11 @@ jobs: strategy: matrix: NXF_VER: - - "21.10.3" + - "22.10.1" - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 05f28000..bbe598f0 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -24,7 +24,7 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - uses: actions/setup-node@v2 + - uses: actions/setup-node@v3 - name: Install Prettier run: npm install -g prettier @prettier/plugin-php @@ -34,9 +34,9 @@ jobs: id: prettier_status run: | if prettier --check ${GITHUB_WORKSPACE}; then - echo "::set-output name=result::pass" + echo "name=result::pass" >> $GITHUB_OUTPUT else - echo "::set-output name=result::fail" + echo "name=result::fail" >> $GITHUB_OUTPUT fi - name: Run 'prettier --write' diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 8a5ce69b..858d622e 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -4,6 +4,8 @@ name: nf-core linting # that the code meets the nf-core guidelines. on: push: + branches: + - dev pull_request: release: types: [published] @@ -12,9 +14,9 @@ jobs: EditorConfig: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: actions/setup-node@v2 + - uses: actions/setup-node@v3 - name: Install editorconfig-checker run: npm install -g editorconfig-checker @@ -25,9 +27,9 @@ jobs: Prettier: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: actions/setup-node@v2 + - uses: actions/setup-node@v3 - name: Install Prettier run: npm install -g prettier @@ -38,7 +40,7 @@ jobs: PythonBlack: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Check code lints with Black uses: psf/black@stable @@ -69,12 +71,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 - - uses: actions/setup-python@v3 + - uses: actions/setup-python@v4 with: python-version: "3.7" architecture: "x64" @@ -97,7 +99,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v3 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 04758f61..39635186 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -18,7 +18,7 @@ jobs: - name: Get PR number id: pr_number - run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)" + run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment uses: marocchino/sticky-pull-request-comment@v2 diff --git a/.prettierignore b/.prettierignore index eb74a574..437d763d 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,5 +1,6 @@ email_template.html adaptivecard.json +slackreport.json .nextflow* work/ data/ @@ -8,3 +9,4 @@ results/ testing/ testing* *.pyc +bin/ diff --git a/CITATION.cff b/CITATION.cff deleted file mode 100644 index 017666c0..00000000 --- a/CITATION.cff +++ /dev/null @@ -1,56 +0,0 @@ -cff-version: 1.2.0 -message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication" -authors: - - family-names: Ewels - given-names: Philip - - family-names: Peltzer - given-names: Alexander - - family-names: Fillinger - given-names: Sven - - family-names: Patel - given-names: Harshil - - family-names: Alneberg - given-names: Johannes - - family-names: Wilm - given-names: Andreas - - family-names: Garcia - given-names: Maxime Ulysse - - family-names: Di Tommaso - given-names: Paolo - - family-names: Nahnsen - given-names: Sven -title: "The nf-core framework for community-curated bioinformatics pipelines." -version: 2.4.1 -doi: 10.1038/s41587-020-0439-x -date-released: 2022-05-16 -url: https://github.com/nf-core/tools -prefered-citation: - type: article - authors: - - family-names: Ewels - given-names: Philip - - family-names: Peltzer - given-names: Alexander - - family-names: Fillinger - given-names: Sven - - family-names: Patel - given-names: Harshil - - family-names: Alneberg - given-names: Johannes - - family-names: Wilm - given-names: Andreas - - family-names: Garcia - given-names: Maxime Ulysse - - family-names: Di Tommaso - given-names: Paolo - - family-names: Nahnsen - given-names: Sven - doi: 10.1038/s41587-020-0439-x - journal: nature biotechnology - start: 276 - end: 278 - title: "The nf-core framework for community-curated bioinformatics pipelines." - issue: 3 - volume: 38 - year: 2020 - url: https://dx.doi.org/10.1038/s41587-020-0439-x diff --git a/README.md b/README.md index ddd4f49a..5aab6a15 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/bacass/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -31,7 +31,7 @@ On release, automated continuous integration tests run the pipeline on a full-si ## Quick Start -1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`) +1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`) 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. diff --git a/assets/slackreport.json b/assets/slackreport.json new file mode 100644 index 00000000..043d02f2 --- /dev/null +++ b/assets/slackreport.json @@ -0,0 +1,34 @@ +{ + "attachments": [ + { + "fallback": "Plain-text summary of the attachment.", + "color": "<% if (success) { %>good<% } else { %>danger<%} %>", + "author_name": "sanger-tol/readmapping v${version} - ${runName}", + "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", + "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", + "fields": [ + { + "title": "Command used to launch the workflow", + "value": "```${commandLine}```", + "short": false + } + <% + if (!success) { %> + , + { + "title": "Full error message", + "value": "```${errorReport}```", + "short": false + }, + { + "title": "Pipeline configuration", + "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>", + "short": false + } + <% } + %> + ], + "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})" + } + ] +} diff --git a/docs/usage.md b/docs/usage.md index dd339d43..d5602abb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -83,9 +83,9 @@ nextflow pull nf-core/bacass It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. -First, go to the [nf-core/bacass releases page](https://github.com/nf-core/bacass/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. +First, go to the [nf-core/bacass releases page](https://github.com/nf-core/bacass/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. -This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. +This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. ## Core Nextflow arguments @@ -95,7 +95,7 @@ This version number will be logged in reports when you run the pipeline, so that Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. When using Biocontainers, most of these software packaging methods pull Docker containers from quay.io e.g [FastQC](https://quay.io/repository/biocontainers/fastqc) except for Singularity which directly downloads Singularity images via https hosted by the [Galaxy project](https://depot.galaxyproject.org/singularity/) and Conda which downloads and installs software locally from [Bioconda](https://bioconda.github.io/). +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. @@ -104,8 +104,11 @@ The pipeline also dynamically loads configurations from [https://github.com/nf-c Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. -If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended. +If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment. +- `test` + - A profile with a complete configuration for automated testing + - Includes links to test data so needs no other parameters - `docker` - A generic configuration profile to be used with [Docker](https://docker.com/) - `singularity` @@ -118,9 +121,6 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. -- `test` - - A profile with a complete configuration for automated testing - - Includes links to test data so needs no other parameters ### `-resume` @@ -169,8 +169,14 @@ Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` ``` +#### For beginners + +A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below. + +#### Advanced option on process level + To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). -We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/software/star/align/main.nf`. +We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`. If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. @@ -189,7 +195,7 @@ process { > > If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. -### Updating containers +### Updating containers (advanced users) The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index b3d092f8..33cd4f6e 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -46,7 +46,6 @@ class NfcoreSchema { 'quiet', 'syslog', 'v', - 'version', // Options for `nextflow run` command 'ansi', diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 27feb009..25a0a74a 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -32,6 +32,25 @@ class NfcoreTemplate { } } + // + // Generate version string + // + public static String version(workflow) { + String version_string = "" + + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string + } + // // Construct and send completion email // @@ -61,7 +80,7 @@ class NfcoreTemplate { misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] - email_fields['version'] = workflow.manifest.version + email_fields['version'] = NfcoreTemplate.version(workflow) email_fields['runName'] = workflow.runName email_fields['success'] = workflow.success email_fields['dateComplete'] = workflow.complete @@ -146,10 +165,10 @@ class NfcoreTemplate { } // - // Construct and send adaptive card - // https://adaptivecards.io + // Construct and send a notification to a web server as JSON + // e.g. Microsoft Teams and Slack // - public static void adaptivecard(workflow, params, summary_params, projectDir, log) { + public static void IM_notification(workflow, params, summary_params, projectDir, log) { def hook_url = params.hook_url def summary = [:] @@ -170,7 +189,7 @@ class NfcoreTemplate { misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] - msg_fields['version'] = workflow.manifest.version + msg_fields['version'] = NfcoreTemplate.version(workflow) msg_fields['runName'] = workflow.runName msg_fields['success'] = workflow.success msg_fields['dateComplete'] = workflow.complete @@ -178,13 +197,16 @@ class NfcoreTemplate { msg_fields['exitStatus'] = workflow.exitStatus msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") msg_fields['projectDir'] = workflow.projectDir msg_fields['summary'] = summary << misc_fields // Render the JSON template def engine = new groovy.text.GStringTemplateEngine() - def hf = new File("$projectDir/assets/adaptivecard.json") + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("$projectDir/assets/${json_path}") def json_template = engine.createTemplate(hf).make(msg_fields) def json_message = json_template.toString() @@ -209,7 +231,7 @@ class NfcoreTemplate { if (workflow.stats.ignoredCount == 0) { log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" } } else { log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" @@ -297,6 +319,7 @@ class NfcoreTemplate { // public static String logo(workflow, monochrome_logs) { Map colors = logColours(monochrome_logs) + String workflow_version = NfcoreTemplate.version(workflow) String.format( """\n ${dashedLine(monochrome_logs)} @@ -305,7 +328,7 @@ class NfcoreTemplate { ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset} + ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} ${dashedLine(monochrome_logs)} """.stripIndent() ) diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 8379896f..5da24bb5 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -19,7 +19,7 @@ class WorkflowMain { } // - // Print help to screen if required + // Generate help string // public static String help(workflow, params, log) { def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" @@ -32,7 +32,7 @@ class WorkflowMain { } // - // Print parameter summary log to screen + // Generate parameter summary log string // public static String paramsSummaryLog(workflow, params, log) { def summary_log = '' @@ -53,15 +53,21 @@ class WorkflowMain { System.exit(0) } - // Validate workflow parameters via the JSON schema - if (params.validate_params) { - NfcoreSchema.validateParameters(workflow, params, log) + // Print workflow version and exit on --version + if (params.version) { + String workflow_version = NfcoreTemplate.version(workflow) + log.info "${workflow.manifest.name} ${workflow_version}" + System.exit(0) } // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params, log) + // Validate workflow parameters via the JSON schema + if (params.validate_params) { + NfcoreSchema.validateParameters(workflow, params, log) + } + // Check that a -profile or Nextflow config has been provided to run the pipeline NfcoreTemplate.checkConfigProvided(workflow, log) diff --git a/modules.json b/modules.json index 80d8edb7..44e747ab 100644 --- a/modules.json +++ b/modules.json @@ -7,15 +7,18 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": ["modules"] } } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 322bd1e9..43f0b971 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -1,5 +1,6 @@ process SAMPLESHEET_CHECK { tag "$samplesheet" + label 'process_single' conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -13,6 +14,9 @@ process SAMPLESHEET_CHECK { path '*.csv' , emit: csv path "versions.yml", emit: versions + when: + task.ext.when == null || task.ext.when + script: // This script is bundled with the pipeline, in nf-core/bacass/bin/ """ check_samplesheet.py \\ diff --git a/nextflow.config b/nextflow.config index 4f42c8c3..a72d8c36 100644 --- a/nextflow.config +++ b/nextflow.config @@ -35,6 +35,7 @@ params { monochrome_logs = false hook_url = null help = false + version = false validate_params = true show_hidden_params = false schema_ignore_params = 'genomes' @@ -81,6 +82,7 @@ profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { params.enable_conda = true + conda.enabled = true docker.enabled = false singularity.enabled = false podman.enabled = false @@ -89,6 +91,7 @@ profiles { } mamba { params.enable_conda = true + conda.enabled = true conda.useMamba = true docker.enabled = false singularity.enabled = false @@ -104,6 +107,9 @@ profiles { shifter.enabled = false charliecloud.enabled = false } + arm { + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + } singularity { singularity.enabled = true singularity.autoMounts = true @@ -185,11 +191,11 @@ dag { manifest { name = 'nf-core/bacass' - author = 'Andreas Wilm, Alexander Peltzer' + author = """Andreas Wilm, Alexander Peltzer""" homePage = 'https://github.com/nf-core/bacass' - description = 'Simple bacterial assembly and annotation' + description = """Simple bacterial assembly and annotation""" mainScript = 'main.nf' - nextflowVersion = '!>=21.10.3' + nextflowVersion = '!>=22.10.1' version = '2.1.0dev' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 8538aaac..317a7e21 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -176,6 +176,12 @@ "fa_icon": "fas fa-question-circle", "hidden": true }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, "publish_dir_mode": { "type": "string", "default": "copy", @@ -217,7 +223,7 @@ "type": "string", "description": "Incoming hook URL for messaging service", "fa_icon": "fas fa-people-group", - "help_text": "Incoming hook URL for messaging service. Currently, only MS Teams is supported.", + "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", "hidden": true }, "multiqc_config": { diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 61a125d6..2f295b1c 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -82,7 +82,7 @@ workflow BACASS { ch_versions = ch_versions.mix(FASTQC.out.versions.first()) CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') + ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml') ) // @@ -102,12 +102,11 @@ workflow BACASS { MULTIQC ( ch_multiqc_files.collect(), - ch_multiqc_config.collect().ifEmpty([]), - ch_multiqc_custom_config.collect().ifEmpty([]), - ch_multiqc_logo.collect().ifEmpty([]) + ch_multiqc_config.toList(), + ch_multiqc_custom_config.toList(), + ch_multiqc_logo.toList() ) multiqc_report = MULTIQC.out.report.toList() - ch_versions = ch_versions.mix(MULTIQC.out.versions) } /* @@ -122,7 +121,7 @@ workflow.onComplete { } NfcoreTemplate.summary(workflow, params, log) if (params.hook_url) { - NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log) + NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) } } From 10134667db97cb25b1cb4469a35453b0974a7df6 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 19 Dec 2022 12:04:59 +0000 Subject: [PATCH 10/21] Template update for nf-core/tools version 2.7.2 --- .github/workflows/fix-linting.yml | 4 +- .github/workflows/linting_comment.yml | 2 +- lib/WorkflowMain.groovy | 2 +- modules.json | 6 +- modules/local/samplesheet_check.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 2 +- .../templates/dumpsoftwareversions.py | 99 ++++++++++--------- modules/nf-core/fastqc/main.nf | 40 +++----- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 3 - nextflow_schema.json | 6 -- workflows/bacass.nf | 2 +- 12 files changed, 82 insertions(+), 88 deletions(-) mode change 100644 => 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index bbe598f0..474f2f76 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -34,9 +34,9 @@ jobs: id: prettier_status run: | if prettier --check ${GITHUB_WORKSPACE}; then - echo "name=result::pass" >> $GITHUB_OUTPUT + echo "result=pass" >> $GITHUB_OUTPUT else - echo "name=result::fail" >> $GITHUB_OUTPUT + echo "result=fail" >> $GITHUB_OUTPUT fi - name: Run 'prettier --write' diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 39635186..0bbcd30f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -18,7 +18,7 @@ jobs: - name: Get PR number id: pr_number - run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT + run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment uses: marocchino/sticky-pull-request-comment@v2 diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 5da24bb5..2ec0947a 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -72,7 +72,7 @@ class WorkflowMain { NfcoreTemplate.checkConfigProvided(workflow, log) // Check that conda channels are set-up correctly - if (params.enable_conda) { + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { Utils.checkCondaChannels(log) } diff --git a/modules.json b/modules.json index 44e747ab..c5beae30 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 43f0b971..c24ecd64 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -2,7 +2,7 @@ process SAMPLESHEET_CHECK { tag "$samplesheet" label 'process_single' - conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) + conda "conda-forge::python=3.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.8.3' : 'quay.io/biocontainers/python:3.8.3' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index cebb6e05..3df21765 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py old mode 100644 new mode 100755 index 787bdb7b..e55b8d43 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -1,5 +1,9 @@ #!/usr/bin/env python + +"""Provide functions to merge multiple versions.yml files.""" + + import platform from textwrap import dedent @@ -7,6 +11,7 @@ def _make_versions_html(versions): + """Generate a tabular HTML output of all versions for MultiQC.""" html = [ dedent( """\\ @@ -45,47 +50,53 @@ def _make_versions_html(versions): return "\\n".join(html) -versions_this_module = {} -versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, -} - -with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - -# aggregate versions by the module name (derived from fully-qualified process name) -versions_by_module = {} -for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - -versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", -} - -versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), -} - -with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) -with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - -with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) +def main(): + """Load all version files and generate merged output.""" + versions_this_module = {} + versions_this_module["${task.process}"] = { + "python": platform.python_version(), + "yaml": yaml.__version__, + } + + with open("$versions") as f: + versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module + + # aggregate versions by the module name (derived from fully-qualified process name) + versions_by_module = {} + for process, process_versions in versions_by_process.items(): + module = process.split(":")[-1] + try: + if versions_by_module[module] != process_versions: + raise AssertionError( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) + except KeyError: + versions_by_module[module] = process_versions + + versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", + "$workflow.manifest.name": "$workflow.manifest.version", + } + + versions_mqc = { + "id": "software_versions", + "section_name": "${workflow.manifest.name} Software Versions", + "section_href": "https://github.com/${workflow.manifest.name}", + "plot_type": "html", + "description": "are collected at run time from the software output.", + "data": _make_versions_html(versions_by_module), + } + + with open("software_versions.yml", "w") as f: + yaml.dump(versions_by_module, f, default_flow_style=False) + with open("software_versions_mqc.yml", "w") as f: + yaml.dump(versions_mqc, f, default_flow_style=False) + + with open("versions.yml", "w") as f: + yaml.dump(versions_this_module, f, default_flow_style=False) + + +if __name__ == "__main__": + main() diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 05730368..9ae58381 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,7 +2,7 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) + conda "bioconda::fastqc=0.11.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : 'quay.io/biocontainers/fastqc:0.11.9--0' }" @@ -20,30 +20,22 @@ process FASTQC { script: def args = task.ext.args ?: '' - // Add soft-links to original FastQs for consistent naming in pipeline def prefix = task.ext.prefix ?: "${meta.id}" - if (meta.single_end) { - """ - [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz - fastqc $args --threads $task.cpus ${prefix}.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ - } else { - """ - [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz - [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz - fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ - } + // Make list of old name and new name pairs to use for renaming in the bash while loop + def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } + def rename_to = old_new_pairs*.join(' ').join(' ') + def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + """ + printf "%s %s\\n" $rename_to | while read old_name new_name; do + [ -f "\${new_name}" ] || ln -s \$old_name \$new_name + done + fastqc $args --threads $task.cpus $renamed_files + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ stub: def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index a8159a57..68f66bea 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,7 +1,7 @@ process MULTIQC { label 'process_single' - conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" diff --git a/nextflow.config b/nextflow.config index a72d8c36..9ecebf05 100644 --- a/nextflow.config +++ b/nextflow.config @@ -39,7 +39,6 @@ params { validate_params = true show_hidden_params = false schema_ignore_params = 'genomes' - enable_conda = false // Config options @@ -81,7 +80,6 @@ try { profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { - params.enable_conda = true conda.enabled = true docker.enabled = false singularity.enabled = false @@ -90,7 +88,6 @@ profiles { charliecloud.enabled = false } mamba { - params.enable_conda = true conda.enabled = true conda.useMamba = true docker.enabled = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 317a7e21..7411c456 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -263,12 +263,6 @@ "description": "Show all params when using `--help`", "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "enable_conda": { - "type": "boolean", - "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.", - "hidden": true, - "fa_icon": "fas fa-bacon" } } } diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 2f295b1c..f0a0c467 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -82,7 +82,7 @@ workflow BACASS { ch_versions = ch_versions.mix(FASTQC.out.versions.first()) CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml') + ch_versions.unique().collectFile(name: 'collated_versions.yml') ) // From 83950897dd32d6bb874389377de0c5e3d88e838e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 28 Apr 2023 14:18:14 +0000 Subject: [PATCH 11/21] Template update for nf-core/tools version 2.8 --- .editorconfig | 2 +- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/PULL_REQUEST_TEMPLATE.md | 3 +- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- .github/workflows/branch.yml | 2 +- .github/workflows/clean-up.yml | 24 ++++ .github/workflows/linting.yml | 2 +- .pre-commit-config.yaml | 5 + README.md | 74 ++++++---- bin/check_samplesheet.py | 3 - conf/base.config | 2 +- conf/igenomes.config | 8 ++ conf/test_full.config | 2 + docs/usage.md | 130 +++++------------- lib/NfcoreSchema.groovy | 4 +- lib/WorkflowBacass.groovy | 12 +- lib/WorkflowMain.groovy | 13 +- main.nf | 1 - modules.json | 4 +- modules/local/samplesheet_check.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 6 +- .../custom/dumpsoftwareversions/meta.yml | 2 + modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/multiqc/meta.yml | 3 +- nextflow.config | 29 +++- tower.yml | 5 + 27 files changed, 193 insertions(+), 157 deletions(-) create mode 100644 .github/workflows/clean-up.yml create mode 100644 .pre-commit-config.yaml create mode 100644 tower.yml diff --git a/.editorconfig b/.editorconfig index b78de6e6..b6b31907 100644 --- a/.editorconfig +++ b/.editorconfig @@ -8,7 +8,7 @@ trim_trailing_whitespace = true indent_size = 4 indent_style = space -[*.{md,yml,yaml,html,css,scss,js,cff}] +[*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 # These files are edited and tested upstream in nf-core/modules diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index cb41a232..d73433ca 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -45,6 +45,6 @@ body: * Nextflow version _(eg. 22.10.1)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ - * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ + * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ * Version of nf-core/bacass _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 0c7eab4a..73441108 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/baca - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md) +- [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 0e1f0216..c0892e5f 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: nf-core/tower-action@v3 + uses: seqeralabs/action-tower-launch@v1 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 5ad2d9b0..c21cbde8 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: nf-core/tower-action@v3 + uses: seqeralabs/action-tower-launch@v1 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index aaaa127d..b711a8eb 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,7 +13,7 @@ jobs: - name: Check PRs if: github.repository == 'nf-core/bacass' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/bacass ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/bacass ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml new file mode 100644 index 00000000..694e90ec --- /dev/null +++ b/.github/workflows/clean-up.yml @@ -0,0 +1,24 @@ +name: "Close user-tagged issues and PRs" +on: + schedule: + - cron: "0 0 * * 0" # Once a week + +jobs: + clean-up: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@v7 + with: + stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." + stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." + close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." + days-before-stale: 30 + days-before-close: 20 + days-before-pr-close: -1 + any-of-labels: "awaiting-changes,awaiting-feedback" + exempt-issue-labels: "WIP" + exempt-pr-labels: "WIP" + repo-token: "${{ secrets.GITHUB_TOKEN }}" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 858d622e..888cb4bc 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.7" + python-version: "3.8" architecture: "x64" - name: Install dependencies diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..0c31cdb9 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,5 @@ +repos: + - repo: https://github.com/pre-commit/mirrors-prettier + rev: "v2.7.1" + hooks: + - id: prettier diff --git a/README.md b/README.md index 5aab6a15..e84435a1 100644 --- a/README.md +++ b/README.md @@ -8,57 +8,71 @@ [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/bacass) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23bacass-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/bacass)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23bacass-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/bacass)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction - +**nf-core/bacass** is a bioinformatics pipeline that ... -**nf-core/bacass** is a bioinformatics best-practice analysis pipeline for Simple bacterial assembly and annotation. - -The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! - - - -On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/bacass/results). - -## Pipeline summary + + 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) -## Quick Start +## Usage + +> **Note** +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +> with `-profile test` before running the workflow on actual data. + + - Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. +Now, you can run the pipeline using: - > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. - > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. - > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. + -4. Start running your own analysis! +```bash +nextflow run nf-core/bacass \ + -profile \ + --input samplesheet.csv \ + --outdir +``` - +> **Warning:** +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those +> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; +> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). - ```bash - nextflow run nf-core/bacass --input samplesheet.csv --outdir --genome GRCh37 -profile - ``` +For more details, please refer to the [usage documentation](https://nf-co.re/bacass/usage) and the [parameter documentation](https://nf-co.re/bacass/parameters). -## Documentation +## Pipeline output -The nf-core/bacass pipeline comes with documentation about the pipeline [usage](https://nf-co.re/bacass/usage), [parameters](https://nf-co.re/bacass/parameters) and [output](https://nf-co.re/bacass/output). +To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/bacass/results) tab on the nf-core website pipeline page. +For more details about the output files and reports, please refer to the +[output documentation](https://nf-co.re/bacass/output). ## Credits diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 11b15572..4a758fe0 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -158,9 +158,6 @@ def sniff_format(handle): peek = read_head(handle) handle.seek(0) sniffer = csv.Sniffer() - if not sniffer.has_header(peek): - logger.critical("The given sample sheet does not appear to contain a header.") - sys.exit(1) dialect = sniffer.sniff(peek) return dialect diff --git a/conf/base.config b/conf/base.config index afca6212..f44a2fae 100644 --- a/conf/base.config +++ b/conf/base.config @@ -15,7 +15,7 @@ process { memory = { check_max( 6.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } - errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' diff --git a/conf/igenomes.config b/conf/igenomes.config index 7a1b3ac6..3f114377 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -36,6 +36,14 @@ params { macs_gsize = "2.7e9" blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" } + 'CHM13' { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" + bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" + gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" + gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" + mito_name = "chrM" + } 'GRCm38' { fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" diff --git a/conf/test_full.config b/conf/test_full.config index d35a88b9..49a3746e 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,6 +10,8 @@ ---------------------------------------------------------------------------------------- */ +cleanup = true + params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index d5602abb..d2ff3701 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -71,6 +71,29 @@ work # Directory containing the nextflow working files # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` +If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. + +Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. + +> ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +> The above pipeline run specified with a params file in yaml format: + +```bash +nextflow run nf-core/bacass -profile docker -params-file params.yaml +``` + +with `params.yaml` containing: + +```yaml +input: './samplesheet.csv' +outdir: './results/' +genome: 'GRCh37' +input: 'data' +<...> +``` + +You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: @@ -87,6 +110,10 @@ First, go to the [nf-core/bacass releases page](https://github.com/nf-core/bacas This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. +To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. + +> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. + ## Core Nextflow arguments > **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). @@ -95,7 +122,7 @@ This version number will be logged in reports when you run the pipeline, so that Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. @@ -119,8 +146,10 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) - `charliecloud` - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) +- `apptainer` + - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `conda` - - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. + - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. ### `-resume` @@ -138,102 +167,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue: - -```console -[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) -Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' - -Caused by: - Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) - -Command executed: - STAR \ - --genomeDir star \ - --readFilesIn WT_REP1_trimmed.fq.gz \ - --runThreadN 2 \ - --outFileNamePrefix WT_REP1. \ - - -Command exit status: - 137 - -Command output: - (empty) - -Command error: - .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. -Work dir: - /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb - -Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` -``` - -#### For beginners - -A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below. - -#### Advanced option on process level - -To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). -We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`. -If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). -The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. -The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. -Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. -The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. - -```nextflow -process { - withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' { - memory = 100.GB - } -} -``` - -> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. -> -> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. - -### Updating containers (advanced users) - -The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. - -1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19) -2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags) -3. Create the custom config accordingly: - - - For Docker: +To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. - ```nextflow - process { - withName: PANGOLIN { - container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` +### Custom Containers - - For Singularity: +In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. - ```nextflow - process { - withName: PANGOLIN { - container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. - - For Conda: +### Custom Tool Arguments - ```nextflow - process { - withName: PANGOLIN { - conda = 'bioconda::pangolin=3.0.5' - } - } - ``` +A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. -> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. ### nf-core/configs diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index 33cd4f6e..9b34804d 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -2,6 +2,7 @@ // This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. // +import nextflow.Nextflow import org.everit.json.schema.Schema import org.everit.json.schema.loader.SchemaLoader import org.everit.json.schema.ValidationException @@ -83,6 +84,7 @@ class NfcoreSchema { 'stub-run', 'test', 'w', + 'with-apptainer', 'with-charliecloud', 'with-conda', 'with-dag', @@ -177,7 +179,7 @@ class NfcoreSchema { } if (has_error) { - System.exit(1) + Nextflow.error('Exiting!') } } diff --git a/lib/WorkflowBacass.groovy b/lib/WorkflowBacass.groovy index c8f87332..4d1261de 100755 --- a/lib/WorkflowBacass.groovy +++ b/lib/WorkflowBacass.groovy @@ -2,6 +2,7 @@ // This file holds several functions specific to the workflow/bacass.nf in the nf-core/bacass pipeline // +import nextflow.Nextflow import groovy.text.SimpleTemplateEngine class WorkflowBacass { @@ -14,8 +15,7 @@ class WorkflowBacass { if (!params.fasta) { - log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - System.exit(1) + Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." } } @@ -61,17 +61,19 @@ class WorkflowBacass { def description_html = engine.createTemplate(methods_text).make(meta) return description_html - }// + } + + // // Exit pipeline if incorrect --genome key provided // private static void genomeExistsError(params, log) { if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + " Currently, the available genome keys are:\n" + " ${params.genomes.keySet().join(", ")}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - System.exit(1) + Nextflow.error(error_string) } } } diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 2ec0947a..b277503a 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -2,6 +2,8 @@ // This file holds several functions specific to the main.nf workflow in the nf-core/bacass pipeline // +import nextflow.Nextflow + class WorkflowMain { // @@ -21,7 +23,7 @@ class WorkflowMain { // // Generate help string // - public static String help(workflow, params, log) { + public static String help(workflow, params) { def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" def help_string = '' help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) @@ -34,7 +36,7 @@ class WorkflowMain { // // Generate parameter summary log string // - public static String paramsSummaryLog(workflow, params, log) { + public static String paramsSummaryLog(workflow, params) { def summary_log = '' summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) @@ -49,7 +51,7 @@ class WorkflowMain { public static void initialise(workflow, params, log) { // Print help to screen if required if (params.help) { - log.info help(workflow, params, log) + log.info help(workflow, params) System.exit(0) } @@ -61,7 +63,7 @@ class WorkflowMain { } // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params, log) + log.info paramsSummaryLog(workflow, params) // Validate workflow parameters via the JSON schema if (params.validate_params) { @@ -81,8 +83,7 @@ class WorkflowMain { // Check input has been provided if (!params.input) { - log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'" - System.exit(1) + Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") } } // diff --git a/main.nf b/main.nf index 3e800210..6b776dd9 100644 --- a/main.nf +++ b/main.nf @@ -4,7 +4,6 @@ nf-core/bacass ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/bacass - Website: https://nf-co.re/bacass Slack : https://nfcore.slack.com/channels/bacass ---------------------------------------------------------------------------------------- diff --git a/modules.json b/modules.json index c5beae30..aff373a9 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543", "installed_by": ["modules"] }, "fastqc": { @@ -17,7 +17,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7", "installed_by": ["modules"] } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index c24ecd64..f2b65abc 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK { conda "conda-forge::python=3.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'quay.io/biocontainers/python:3.8.3' }" + 'biocontainers/python:3.8.3' }" input: path samplesheet diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 3df21765..800a6099 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 60b546a0..c32657de 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,7 +1,9 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: - custom + - dump - version tools: - custom: diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 68f66bea..4b604749 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index ebc29b27..f93b5ee5 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,3 +1,4 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: MultiQC description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: @@ -37,7 +38,7 @@ output: description: MultiQC report file pattern: "multiqc_report.html" - data: - type: dir + type: directory description: MultiQC data dir pattern: "multiqc_data" - plots: diff --git a/nextflow.config b/nextflow.config index 9ecebf05..5202604a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -78,7 +78,11 @@ try { profiles { - debug { process.beforeScript = 'echo $HOSTNAME' } + debug { + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false + } conda { conda.enabled = true docker.enabled = false @@ -86,6 +90,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } mamba { conda.enabled = true @@ -95,14 +100,18 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } docker { docker.enabled = true + docker.registry = 'quay.io' docker.userEmulation = true + conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' @@ -110,31 +119,49 @@ profiles { singularity { singularity.enabled = true singularity.autoMounts = true + conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } podman { podman.enabled = true + podman.registry = 'quay.io' + conda.enabled = false docker.enabled = false singularity.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } shifter { shifter.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false charliecloud.enabled = false + apptainer.enabled = false } charliecloud { charliecloud.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false + apptainer.enabled = false + } + apptainer { + apptainer.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } gitpod { executor.name = 'local' diff --git a/tower.yml b/tower.yml new file mode 100644 index 00000000..787aedfe --- /dev/null +++ b/tower.yml @@ -0,0 +1,5 @@ +reports: + multiqc_report.html: + display: "MultiQC HTML report" + samplesheet.csv: + display: "Auto-created samplesheet with collated metadata and FASTQ paths" From 73a07e93c36e5edc84f8a87775c6a81a54aa37df Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 30 Jun 2023 16:12:48 +0000 Subject: [PATCH 12/21] Template update for nf-core/tools version 2.9 --- .github/CONTRIBUTING.md | 1 - .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/workflows/awsfulltest.yml | 11 +- .github/workflows/awstest.yml | 10 +- .github/workflows/ci.yml | 2 +- .gitpod.yml | 5 + CITATIONS.md | 6 + README.md | 6 +- assets/methods_description_template.yml | 12 +- assets/multiqc_config.yml | 4 +- assets/nf-core-bacass_logo_light.png | Bin 11313 -> 71089 bytes assets/slackreport.json | 2 +- conf/test_full.config | 2 - docs/usage.md | 6 +- lib/NfcoreSchema.groovy | 530 ------------------------ lib/NfcoreTemplate.groovy | 2 +- lib/WorkflowBacass.groovy | 45 +- lib/WorkflowMain.groovy | 37 -- main.nf | 16 + nextflow.config | 52 ++- nextflow_schema.json | 36 +- workflows/bacass.nf | 25 +- 22 files changed, 175 insertions(+), 637 deletions(-) delete mode 100755 lib/NfcoreSchema.groovy diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 33b89e71..b9535f70 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -116,4 +116,3 @@ To get started: Devcontainer specs: - [DevContainer config](.devcontainer/devcontainer.json) -- [Dockerfile](.devcontainer/Dockerfile) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index d73433ca..8f319341 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -42,7 +42,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 22.10.1)_ + * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index c0892e5f..eac50545 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -22,13 +22,18 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bacass/work-${{ github.sha }} parameters: | { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-${{ github.sha }}" } - profiles: test_full,aws_tower + profiles: test_full + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index c21cbde8..5ff8ad1a 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,18 +12,22 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bacass/work-${{ github.sha }} parameters: | { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-test-${{ github.sha }}" } - profiles: test,aws_tower + profiles: test + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c91c0fb8..c29f9a8c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: - name: Check out pipeline code diff --git a/.gitpod.yml b/.gitpod.yml index 85d95ecc..25488dcc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,9 @@ image: nfcore/gitpod:latest +tasks: + - name: Update Nextflow and setup pre-commit + command: | + pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack diff --git a/CITATIONS.md b/CITATIONS.md index e3a69e9b..4954dd4b 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,10 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools @@ -31,5 +34,8 @@ - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. + - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/README.md b/README.md index e84435a1..b39aae8b 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/bacass/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -66,11 +66,11 @@ nextflow run nf-core/bacass \ > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). -For more details, please refer to the [usage documentation](https://nf-co.re/bacass/usage) and the [parameter documentation](https://nf-co.re/bacass/parameters). +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/bacass/usage) and the [parameter documentation](https://nf-co.re/bacass/parameters). ## Pipeline output -To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/bacass/results) tab on the nf-core website pipeline page. +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/bacass/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/bacass/output). diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index a19f3abb..b0024760 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,17 +3,21 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/bacass Methods Description" section_href: "https://github.com/nf-core/bacass" plot_type: "html" -## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline +## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

    Methods

    -

    Data was processed using nf-core/bacass v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

    +

    Data was processed using nf-core/bacass v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

    The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

    ${workflow.commandLine}
    +

    ${tool_citations}

    References

      -
    • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
      • -
    • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
      • +
    • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
      • +
    • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
      • +
    • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
      • +
    • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
      • + ${tool_bibliography}
    Notes:
    diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 5217b52e..d871ffc7 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/bacass + This report has been generated by the nf-core/bacass analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-bacass-methods-description": order: -1000 diff --git a/assets/nf-core-bacass_logo_light.png b/assets/nf-core-bacass_logo_light.png index 644f00d9651b8d8ad5c1b031e9a6a53215a3eb05..6a16bb9278b3c2d03c07466d2df425c7495cc311 100644 GIT binary patch literal 71089 zcmeEt`9IX_`~RRQS?ZKSWhn*~p=96c5GGq9OZHNfecuPCQz(&w!1jG0qM))u18{N;szxKLnntC7*Z0~7*=;B1!jv^4p5Gb_^hQ29NgTYTSd@O|5 zS3HI44fR<@BwC_WweNAg^K`t?ay|Ua^`zuS;o*5X;p5j0nLR_3TdTw-*C$<<{Vk$; z9`%au>-b1%=CCl=x~!Jp!Br{RFpzjKp!3X+Tb;*QRKss@Kb){h^c+@seV?p-3zMBT zv9)Zlu({<`v3Pc z_~QTk@G~L)&kz6ShyTBGp!b^mFYH1%8g&}PE+NMRdy{Rgwkaa9QvrRQY2HJz)6`6H z9;J$!8p?T$p0J;N*Ye!J#ykH8M)iUCxVX5E!@pK|Rzc1t45Gxe-2E^GvsRWhY(8G+ zqQw!LH!;zIl^)J$8$X^IcCItbD!;xEnF(K*M&+X@JSfW~(%%?AjAD}I{FvT)!b;+< zT`3RVvHyDV#tr{F?pFSzX|tN{P8k1QHN6RI-9sVD@-lUEm%l0Eg`Uqb{CpIznVgoC zqUmmd=@Irb{U+;BnnF@S4JpEd=f8=bxA|}L4A?vsm9JMY?xEj%PSrz{(B9T6zCrD{ 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${runName}", + "author_name": "nf-core/bacass v${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/test_full.config b/conf/test_full.config index 49a3746e..d35a88b9 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,8 +10,6 @@ ---------------------------------------------------------------------------------------- */ -cleanup = true - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index d2ff3701..c6622965 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/bacass --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run nf-core/bacass --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -76,7 +76,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -> The above pipeline run specified with a params file in yaml format: + +The above pipeline run specified with a params file in yaml format: ```bash nextflow run nf-core/bacass -profile docker -params-file params.yaml @@ -88,7 +89,6 @@ with `params.yaml` containing: input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' -input: 'data' <...> ``` diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy deleted file mode 100755 index 9b34804d..00000000 --- a/lib/NfcoreSchema.groovy +++ /dev/null @@ -1,530 +0,0 @@ -// -// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. -// - -import nextflow.Nextflow -import org.everit.json.schema.Schema -import org.everit.json.schema.loader.SchemaLoader -import org.everit.json.schema.ValidationException -import org.json.JSONObject -import org.json.JSONTokener -import org.json.JSONArray -import groovy.json.JsonSlurper -import groovy.json.JsonBuilder - -class NfcoreSchema { - - // - // Resolve Schema path relative to main workflow directory - // - public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') { - return "${workflow.projectDir}/${schema_filename}" - } - - // - // Function to loop over all parameters defined in schema and check - // whether the given parameters adhere to the specifications - // - /* groovylint-disable-next-line UnusedPrivateMethodParameter */ - public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') { - def has_error = false - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Check for nextflow core params and unexpected params - def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text - def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') - def nf_params = [ - // Options for base `nextflow` command - 'bg', - 'c', - 'C', - 'config', - 'd', - 'D', - 'dockerize', - 'h', - 'log', - 'q', - 'quiet', - 'syslog', - 'v', - - // Options for `nextflow run` command - 'ansi', - 'ansi-log', - 'bg', - 'bucket-dir', - 'c', - 'cache', - 'config', - 'dsl2', - 'dump-channels', - 'dump-hashes', - 'E', - 'entry', - 'latest', - 'lib', - 'main-script', - 'N', - 'name', - 'offline', - 'params-file', - 'pi', - 'plugins', - 'poll-interval', - 'pool-size', - 'profile', - 'ps', - 'qs', - 'queue-size', - 'r', - 'resume', - 'revision', - 'stdin', - 'stub', - 'stub-run', - 'test', - 'w', - 'with-apptainer', - 'with-charliecloud', - 'with-conda', - 'with-dag', - 'with-docker', - 'with-mpi', - 'with-notification', - 'with-podman', - 'with-report', - 'with-singularity', - 'with-timeline', - 'with-tower', - 'with-trace', - 'with-weblog', - 'without-docker', - 'without-podman', - 'work-dir' - ] - def unexpectedParams = [] - - // Collect expected parameters from the schema - def expectedParams = [] - def enums = [:] - for (group in schemaParams) { - for (p in group.value['properties']) { - expectedParams.push(p.key) - if (group.value['properties'][p.key].containsKey('enum')) { - enums[p.key] = group.value['properties'][p.key]['enum'] - } - } - } - - for (specifiedParam in params.keySet()) { - // nextflow params - if (nf_params.contains(specifiedParam)) { - log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'" - has_error = true - } - // unexpected params - def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params' - def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() } - def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase() - def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase)) - if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) { - // Temporarily remove camelCase/camel-case params #1035 - def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()} - if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){ - unexpectedParams.push(specifiedParam) - } - } - } - - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Validate parameters against the schema - InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream() - JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream)) - - // Remove anything that's in params.schema_ignore_params - raw_schema = removeIgnoredParams(raw_schema, params) - - Schema schema = SchemaLoader.load(raw_schema) - - // Clean the parameters - def cleanedParams = cleanParameters(params) - - // Convert to JSONObject - def jsonParams = new JsonBuilder(cleanedParams) - JSONObject params_json = new JSONObject(jsonParams.toString()) - - // Validate - try { - schema.validate(params_json) - } catch (ValidationException e) { - println '' - log.error 'ERROR: Validation of pipeline parameters failed!' - JSONObject exceptionJSON = e.toJSON() - printExceptions(exceptionJSON, params_json, log, enums) - println '' - has_error = true - } - - // Check for unexpected parameters - if (unexpectedParams.size() > 0) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - println '' - def warn_msg = 'Found unexpected parameters:' - for (unexpectedParam in unexpectedParams) { - warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}" - } - log.warn warn_msg - log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}" - println '' - } - - if (has_error) { - Nextflow.error('Exiting!') - } - } - - // - // Beautify parameters for --help - // - public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - Integer num_hidden = 0 - String output = '' - output += 'Typical pipeline command:\n\n' - output += " ${colors.cyan}${command}${colors.reset}\n\n" - Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - Integer max_chars = paramsMaxChars(params_map) + 1 - Integer desc_indent = max_chars + 14 - Integer dec_linewidth = 160 - desc_indent - for (group in params_map.keySet()) { - Integer num_params = 0 - String group_output = colors.underlined + colors.bold + group + colors.reset + '\n' - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (group_params.get(param).hidden && !params.show_hidden_params) { - num_hidden += 1 - continue; - } - def type = '[' + group_params.get(param).type + ']' - def description = group_params.get(param).description - def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : '' - def description_default = description + colors.dim + defaultValue + colors.reset - // Wrap long description texts - // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap - if (description_default.length() > dec_linewidth){ - List olines = [] - String oline = "" // " " * indent - description_default.split(" ").each() { wrd -> - if ((oline.size() + wrd.size()) <= dec_linewidth) { - oline += wrd + " " - } else { - olines += oline - oline = wrd + " " - } - } - olines += oline - description_default = olines.join("\n" + " " * desc_indent) - } - group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n' - num_params += 1 - } - group_output += '\n' - if (num_params > 0){ - output += group_output - } - } - if (num_hidden > 0){ - output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset - } - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Groovy Map summarising parameters/workflow options used by the pipeline - // - public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') { - // Get a selection of core Nextflow workflow options - def Map workflow_summary = [:] - if (workflow.revision) { - workflow_summary['revision'] = workflow.revision - } - workflow_summary['runName'] = workflow.runName - if (workflow.containerEngine) { - workflow_summary['containerEngine'] = workflow.containerEngine - } - if (workflow.container) { - workflow_summary['container'] = workflow.container - } - workflow_summary['launchDir'] = workflow.launchDir - workflow_summary['workDir'] = workflow.workDir - workflow_summary['projectDir'] = workflow.projectDir - workflow_summary['userName'] = workflow.userName - workflow_summary['profile'] = workflow.profile - workflow_summary['configFiles'] = workflow.configFiles.join(', ') - - // Get pipeline parameters defined in JSON Schema - def Map params_summary = [:] - def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - for (group in params_map.keySet()) { - def sub_params = new LinkedHashMap() - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (params.containsKey(param)) { - def params_value = params.get(param) - def schema_value = group_params.get(param).default - def param_type = group_params.get(param).type - if (schema_value != null) { - if (param_type == 'string') { - if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) { - def sub_string = schema_value.replace('\$projectDir', '') - sub_string = sub_string.replace('\${projectDir}', '') - if (params_value.contains(sub_string)) { - schema_value = params_value - } - } - if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) { - def sub_string = schema_value.replace('\$params.outdir', '') - sub_string = sub_string.replace('\${params.outdir}', '') - if ("${params.outdir}${sub_string}" == params_value) { - schema_value = params_value - } - } - } - } - - // We have a default in the schema, and this isn't it - if (schema_value != null && params_value != schema_value) { - sub_params.put(param, params_value) - } - // No default in the schema, and this isn't empty - else if (schema_value == null && params_value != "" && params_value != null && params_value != false) { - sub_params.put(param, params_value) - } - } - } - params_summary.put(group, sub_params) - } - return [ 'Core Nextflow options' : workflow_summary ] << params_summary - } - - // - // Beautify parameters for summary and return as string - // - public static String paramsSummaryLog(workflow, params) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - String output = '' - def params_map = paramsSummaryMap(workflow, params) - def max_chars = paramsMaxChars(params_map) - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - if (group_params) { - output += colors.bold + group + colors.reset + '\n' - for (param in group_params.keySet()) { - output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n' - } - output += '\n' - } - } - output += "!! Only displaying parameters that differ from the pipeline defaults !!\n" - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Loop over nested exceptions and print the causingException - // - private static void printExceptions(ex_json, params_json, log, enums, limit=5) { - def causingExceptions = ex_json['causingExceptions'] - if (causingExceptions.length() == 0) { - def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/ - // Missing required param - if (m.matches()) { - log.error "* Missing required parameter: --${m[0][1]}" - } - // Other base-level error - else if (ex_json['pointerToViolation'] == '#') { - log.error "* ${ex_json['message']}" - } - // Error with specific param - else { - def param = ex_json['pointerToViolation'] - ~/^#\// - def param_val = params_json[param].toString() - if (enums.containsKey(param)) { - def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices" - if (enums[param].size() > limit) { - log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )" - } else { - log.error "${error_msg}: ${enums[param].join(', ')})" - } - } else { - log.error "* --${param}: ${ex_json['message']} (${param_val})" - } - } - } - for (ex in causingExceptions) { - printExceptions(ex, params_json, log, enums) - } - } - - // - // Remove an element from a JSONArray - // - private static JSONArray removeElement(json_array, element) { - def list = [] - int len = json_array.length() - for (int i=0;i - if(raw_schema.keySet().contains('definitions')){ - raw_schema.definitions.each { definition -> - for (key in definition.keySet()){ - if (definition[key].get("properties").keySet().contains(ignore_param)){ - // Remove the param to ignore - definition[key].get("properties").remove(ignore_param) - // If the param was required, change this - if (definition[key].has("required")) { - def cleaned_required = removeElement(definition[key].required, ignore_param) - definition[key].put("required", cleaned_required) - } - } - } - } - } - if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) { - raw_schema.get("properties").remove(ignore_param) - } - if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) { - def cleaned_required = removeElement(raw_schema.required, ignore_param) - raw_schema.put("required", cleaned_required) - } - } - return raw_schema - } - - // - // Clean and check parameters relative to Nextflow native classes - // - private static Map cleanParameters(params) { - def new_params = params.getClass().newInstance(params) - for (p in params) { - // remove anything evaluating to false - if (!p['value']) { - new_params.remove(p.key) - } - // Cast MemoryUnit to String - if (p['value'].getClass() == nextflow.util.MemoryUnit) { - new_params.replace(p.key, p['value'].toString()) - } - // Cast Duration to String - if (p['value'].getClass() == nextflow.util.Duration) { - new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day")) - } - // Cast LinkedHashMap to String - if (p['value'].getClass() == LinkedHashMap) { - new_params.replace(p.key, p['value'].toString()) - } - } - return new_params - } - - // - // This function tries to read a JSON params file - // - private static LinkedHashMap paramsLoad(String json_schema) { - def params_map = new LinkedHashMap() - try { - params_map = paramsRead(json_schema) - } catch (Exception e) { - println "Could not read parameters settings from JSON. $e" - params_map = new LinkedHashMap() - } - return params_map - } - - // - // Method to actually read in JSON file using Groovy. - // Group (as Key), values are all parameters - // - Parameter1 as Key, Description as Value - // - Parameter2 as Key, Description as Value - // .... - // Group - // - - private static LinkedHashMap paramsRead(String json_schema) throws Exception { - def json = new File(json_schema).text - def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions') - def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties') - /* Tree looks like this in nf-core schema - * definitions <- this is what the first get('definitions') gets us - group 1 - title - description - properties - parameter 1 - type - description - parameter 2 - type - description - group 2 - title - description - properties - parameter 1 - type - description - * properties <- parameters can also be ungrouped, outside of definitions - parameter 1 - type - description - */ - - // Grouped params - def params_map = new LinkedHashMap() - schema_definitions.each { key, val -> - def Map group = schema_definitions."$key".properties // Gets the property object of the group - def title = schema_definitions."$key".title - def sub_params = new LinkedHashMap() - group.each { innerkey, value -> - sub_params.put(innerkey, value) - } - params_map.put(title, sub_params) - } - - // Ungrouped params - def ungrouped_params = new LinkedHashMap() - schema_properties.each { innerkey, value -> - ungrouped_params.put(innerkey, value) - } - params_map.put("Other parameters", ungrouped_params) - - return params_map - } - - // - // Get maximum number of characters across all parameter names - // - private static Integer paramsMaxChars(params_map) { - Integer max_chars = 0 - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (param.size() > max_chars) { - max_chars = param.size() - } - } - } - return max_chars - } -} diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 25a0a74a..408951ae 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -128,7 +128,7 @@ class NfcoreTemplate { def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] def sf = new File("$projectDir/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) diff --git a/lib/WorkflowBacass.groovy b/lib/WorkflowBacass.groovy index 4d1261de..b9a48aa4 100755 --- a/lib/WorkflowBacass.groovy +++ b/lib/WorkflowBacass.groovy @@ -11,6 +11,7 @@ class WorkflowBacass { // Check and validate parameters // public static void initialise(params, log) { + genomeExistsError(params, log) @@ -46,15 +47,57 @@ class WorkflowBacass { return yaml_file_text } - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // + // Generate methods description for MultiQC + // + + public static String toolCitationText(params) { + + // TODO Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text + } + + public static String toolBibliographyText(params) { + + // TODO Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "

  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = run_workflow.toMap() meta["manifest_map"] = run_workflow.manifest.toMap() + // Pipeline DOI meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + //meta["tool_bibliography"] = toolBibliographyText(params) + + def methods_text = mqc_methods_yaml.text def engine = new SimpleTemplateEngine() diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index b277503a..76691b66 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -20,40 +20,11 @@ class WorkflowMain { " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } - // - // Generate help string - // - public static String help(workflow, params) { - def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - def help_string = '' - help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) - help_string += NfcoreSchema.paramsHelp(workflow, params, command) - help_string += '\n' + citation(workflow) + '\n' - help_string += NfcoreTemplate.dashedLine(params.monochrome_logs) - return help_string - } - - // - // Generate parameter summary log string - // - public static String paramsSummaryLog(workflow, params) { - def summary_log = '' - summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) - summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) - summary_log += '\n' + citation(workflow) + '\n' - summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs) - return summary_log - } // // Validate parameters and print summary to screen // public static void initialise(workflow, params, log) { - // Print help to screen if required - if (params.help) { - log.info help(workflow, params) - System.exit(0) - } // Print workflow version and exit on --version if (params.version) { @@ -62,14 +33,6 @@ class WorkflowMain { System.exit(0) } - // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params) - - // Validate workflow parameters via the JSON schema - if (params.validate_params) { - NfcoreSchema.validateParameters(workflow, params, log) - } - // Check that a -profile or Nextflow config has been provided to run the pipeline NfcoreTemplate.checkConfigProvided(workflow, log) diff --git a/main.nf b/main.nf index 6b776dd9..4e175f76 100644 --- a/main.nf +++ b/main.nf @@ -25,6 +25,22 @@ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { validateParameters; paramsHelp } from 'plugin/nf-validation' + +// Print help message if needed +if (params.help) { + def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) + def citation = '\n' + WorkflowMain.citation(workflow) + '\n' + def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) + System.exit(0) +} + +// Validate input parameters +if (params.validate_params) { + validateParameters() +} + WorkflowMain.initialise(workflow, params, log) /* diff --git a/nextflow.config b/nextflow.config index 5202604a..a054b40e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,12 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null - - // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false + + // MultiQC options multiqc_config = null multiqc_title = null @@ -27,7 +27,6 @@ params { // Boilerplate options outdir = null - tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null email_on_fail = null @@ -36,19 +35,15 @@ params { hook_url = null help = false version = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes' - // Config options + config_profile_name = null + config_profile_description = null custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_description = null config_profile_contact = null config_profile_url = null - config_profile_name = null - + // Max resource options // Defaults only, expecting to be overwritten @@ -56,6 +51,13 @@ params { max_cpus = 16 max_time = '240.h' + // Schema validation default options + validationFailUnrecognisedParams = false + validationLenientMode = false + validationSchemaIgnoreParams = 'genomes' + validationShowHiddenParams = false + validate_params = true + } // Load base.config by default for all pipelines @@ -75,13 +77,11 @@ try { // } catch (Exception e) { // System.err.println("WARNING: Could not load nf-core/config/bacass profiles: ${params.custom_config_base}/pipeline/bacass.config") // } - - profiles { debug { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' - cleanup = false + cleanup = false } conda { conda.enabled = true @@ -104,7 +104,6 @@ profiles { } docker { docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false @@ -128,7 +127,6 @@ profiles { } podman { podman.enabled = true - podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false @@ -172,6 +170,18 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Nextflow plugins +plugins { + id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} // Load igenomes.config if required if (!params.igenomes_ignore) { @@ -179,8 +189,6 @@ if (!params.igenomes_ignore) { } else { params.genomes = [:] } - - // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -198,19 +206,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" } report { enabled = true - file = "${params.tracedir}/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" } trace { enabled = true - file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" } dag { enabled = true - file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" } manifest { @@ -219,7 +227,7 @@ manifest { homePage = 'https://github.com/nf-core/bacass' description = """Simple bacterial assembly and annotation""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' + nextflowVersion = '!>=23.04.0' version = '2.1.0dev' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 7411c456..083ee384 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,9 +15,9 @@ "input": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", - "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/bacass/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" @@ -57,6 +57,7 @@ "fasta": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/plain", "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", "description": "Path to FASTA genome file.", @@ -157,7 +158,7 @@ "description": "Maximum amount of time that can be requested for any single job.", "default": "240.h", "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", "hidden": true, "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" } @@ -174,12 +175,14 @@ "type": "boolean", "description": "Display help text.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "version": { "type": "boolean", "description": "Display version and exit.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "publish_dir_mode": { @@ -203,6 +206,7 @@ "type": "boolean", "description": "Send plain-text email instead of HTML.", "fa_icon": "fas fa-remove-format", + "default": false, "hidden": true }, "max_multiqc_email_size": { @@ -217,6 +221,7 @@ "type": "boolean", "description": "Do not use coloured log outputs.", "fa_icon": "fas fa-palette", + "default": false, "hidden": true }, "hook_url": { @@ -228,6 +233,7 @@ }, "multiqc_config": { "type": "string", + "format": "file-path", "description": "Custom config file to supply to MultiQC.", "fa_icon": "fas fa-cog", "hidden": true @@ -243,13 +249,6 @@ "description": "Custom MultiQC yaml file containing HTML including a methods description.", "fa_icon": "fas fa-cog" }, - "tracedir": { - "type": "string", - "description": "Directory to keep pipeline Nextflow logs and reports.", - "default": "${params.outdir}/pipeline_info", - "fa_icon": "fas fa-cogs", - "hidden": true - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", @@ -257,12 +256,29 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "show_hidden_params": { + "validationShowHiddenParams": { "type": "boolean", "fa_icon": "far fa-eye-slash", "description": "Show all params when using `--help`", + "default": false, "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + }, + "validationFailUnrecognisedParams": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters fails when an unrecognised parameter is found.", + "default": false, + "hidden": true, + "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + }, + "validationLenientMode": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters in lenient more.", + "default": false, + "hidden": true, + "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." } } } diff --git a/workflows/bacass.nf b/workflows/bacass.nf index f0a0c467..506a68dd 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -1,21 +1,19 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE INPUTS + PRINT PARAMS SUMMARY ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) +include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' -// Validate input parameters -WorkflowBacass.initialise(params, log) +def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) +def citation = '\n' + WorkflowMain.citation(workflow) + '\n' +def summary_params = paramsSummaryMap(workflow) -// TODO nf-core: Add all file path parameters for the pipeline to the list below -// Check input path parameters to see if they exist -def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ] -for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } +// Print parameter summary log to screen +log.info logo + paramsSummaryLog(workflow) + citation -// Check mandatory parameters -if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } +WorkflowBacass.initialise(params, log) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -69,9 +67,12 @@ workflow BACASS { // SUBWORKFLOW: Read in samplesheet, validate and stage input files // INPUT_CHECK ( - ch_input + file(params.input) ) ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") + // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ + // ! There is currently no tooling to help you write a sample sheet schema // // MODULE: Run FastQC @@ -91,7 +92,7 @@ workflow BACASS { workflow_summary = WorkflowBacass.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) - methods_description = WorkflowBacass.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + methods_description = WorkflowBacass.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) ch_methods_description = Channel.value(methods_description) ch_multiqc_files = Channel.empty() From cd125df0264a8618fba9d808e27b5bd703664de7 Mon Sep 17 00:00:00 2001 From: Dani VM Date: Mon, 11 Sep 2023 17:51:11 +0200 Subject: [PATCH 13/21] fix nf-core linting --- CHANGELOG.md | 163 ++++++++++++++++++------------------ CITATIONS.md | 33 +++++--- README.md | 2 +- assets/test_config_dfast.py | 54 ++++-------- docs/output.md | 119 +++++++++++++------------- docs/usage.md | 14 ++-- nextflow_schema.json | 55 +++--------- 7 files changed, 202 insertions(+), 238 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 081d0a71..3bccdc38 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,12 +5,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v2.0.1dev nf-core/bacass: "Navy Steel Swordfish" - 2023/09/11 -This version merges the nf-core template update v2.9. It also updates modules or dependencies to make them work with the new template. +This version merges the nf-core template update v2.9. It also updates modules or dependencies to make them work with the new template. ### `Changed` -* [#84](https://github.com/nf-core/bacass/pull/84) & [#85](https://github.com/nf-core/bacass/issues/85) - Update nf-core/bacass to the new nf-core 2.0 `TEMPLATE`. -* [#61](https://github.com/nf-core/bacass/issues/61) - Update local/modules to nf-core/modules (detailed below). +- [#84](https://github.com/nf-core/bacass/pull/84) & [#85](https://github.com/nf-core/bacass/issues/85) - Update nf-core/bacass to the new nf-core 2.0 `TEMPLATE`. + +- [#61](https://github.com/nf-core/bacass/issues/61) - Update local/modules to nf-core/modules (detailed below). ### `Added` @@ -19,76 +20,76 @@ This version merges the nf-core template update v2.9. It also updates modules or ### `Fixed` -* Fixed modules - - Medaka: Medaka last version (see version update below) doesn't allow gzip compressed files. Add bgzip compression instead. - - Dfast: fix overwriting issues detected when copying sample files from `work/` to `results/` +- Fixed modules + - Medaka: Medaka last version (see version update below) doesn't allow gzip compressed files. Add bgzip compression instead. + - Dfast: fix overwriting issues detected when copying sample files from `work/` to `results/` ### `Dependencies` -* [#61](https://github.com/nf-core/bacass/issues/61) - Update a bunch of local/modules to nf-core/modules plus version update. +- [#61](https://github.com/nf-core/bacass/issues/61) - Update a bunch of local/modules to nf-core/modules plus version update. - - Canu (v2.1.1 → v2.2) - - Minimap2 (v2.21 → v2.24) - - Miniasm - - Racon + - Canu (v2.1.1 → v2.2) + - Minimap2 (v2.21 → v2.24) + - Miniasm + - Racon -* [#84](https://github.com/nf-core/bacass/pull/84) Update already nf-core modules - - Fastqc - - Samtools (v1.13 → v1.17) - - Kraken2 (v2.1.1 → v2.1.2) - - Quast (v5.0.2 → 5.2.0) - - Prokka - - Multiqc (v1.10.1 → v1.15) +- [#84](https://github.com/nf-core/bacass/pull/84) Update already nf-core modules -* Refactor `local/modules` making them follow nf-core v2.9 structure/fashion. + - Fastqc + - Samtools (v1.13 → v1.17) + - Kraken2 (v2.1.1 → v2.1.2) + - Quast (v5.0.2 → 5.2.0) + - Prokka + - Multiqc (v1.10.1 → v1.15) - - Dfast - - Medaka - - Nanoplot (v1.38.0 → v1.41.6) - - Nanopolish (v0.13.2-5 → 0.14.0) - - Pycoqc - - Unicycler +- Refactor `local/modules` making them follow nf-core v2.9 structure/fashion. -### `Deprecated` + - Dfast + - Medaka + - Nanoplot (v1.38.0 → v1.41.6) + - Nanopolish (v0.13.2-5 → 0.14.0) + - Pycoqc + - Unicycler -* [#61](https://github.com/nf-core/bacass/issues/61) - Replace depecated modules with nf-core/modules. +### `Deprecated` - - Replace `local/get_software_versions.nf` with `nf-core/custom/dumpsoftwareversions.nf` - - Replace `local/skewer` by `nf-core/fastp` and wrap fastqc plus fastp into `subworkflows/nf-core/fastq_trim_fastp_fastqc` - - Replace `local/nanoplot` by local/nanoplot_custom (using as template nf-core/nanoplot). +- [#61](https://github.com/nf-core/bacass/issues/61) - Replace depecated modules with nf-core/modules. + - Replace `local/get_software_versions.nf` with `nf-core/custom/dumpsoftwareversions.nf` + - Replace `local/skewer` by `nf-core/fastp` and wrap fastqc plus fastp into `subworkflows/nf-core/fastq_trim_fastp_fastqc` + - Replace `local/nanoplot` by local/nanoplot_custom (using as template nf-core/nanoplot). ## v2.0.0 nf-core/bacass: "Navy Steel Swordfish" 2021/08/27 ### `Changed` -* [#56](https://github.com/nf-core/bacass/pull/56) - Switched to DSL2 & update to new nf-core 2.1 `TEMPLATE` -* [#56](https://github.com/nf-core/bacass/pull/56) - `--krakendb` now expects a `.tar.gz`/`.tgz` (compressed tar archive) directly from `https://benlangmead.github.io/aws-indexes/k2` instead of an uncompressed folder. +- [#56](https://github.com/nf-core/bacass/pull/56) - Switched to DSL2 & update to new nf-core 2.1 `TEMPLATE` +- [#56](https://github.com/nf-core/bacass/pull/56) - `--krakendb` now expects a `.tar.gz`/`.tgz` (compressed tar archive) directly from `https://benlangmead.github.io/aws-indexes/k2` instead of an uncompressed folder. ### `Added` -* [#56](https://github.com/nf-core/bacass/pull/56) - Added full size test dataset, two Zetaproteobacteria sequenced with Illumina MiSeq Reagent Kit V2, PE250, 3 to 4 million read pairs. +- [#56](https://github.com/nf-core/bacass/pull/56) - Added full size test dataset, two Zetaproteobacteria sequenced with Illumina MiSeq Reagent Kit V2, PE250, 3 to 4 million read pairs. ### `Fixed` -* [#51](https://github.com/nf-core/bacass/issues/51) - Fixed Unicycler +- [#51](https://github.com/nf-core/bacass/issues/51) - Fixed Unicycler ### `Dependencies` -* [#56](https://github.com/nf-core/bacass/pull/56) - Updated a bunch of dependencies (unchanged: FastQC, Miniasm, Prokka, Porechop, QUAST) - * Unicycler from 0.4.4 to 0.4.8 - * Kraken2 from 2.0.9beta to 2.1.1 - * MultiQC from 1.9 to 1.10.1 - * PYCOQC from 2.5.0.23 to 2.5.2 - * Samtools from 1.11 to 1.13 - * Canu from 2.0 to 2.1.1-2 - * dfast from 1.2.10 to 1.2.14 - * Medaka from 1.1.2 to 1.4.3-0 - * Minimap 2 from 2.17 to 2.21 - * Nanoplot from 1.32.1 to 1.38.0 - * Nanopolish from 0.13.2 to 0.13.2-5 - * Racon from 1.4.13 to 1.4.20-1 - * Skewer from 0.2.2 to 0.2.2-3 +- [#56](https://github.com/nf-core/bacass/pull/56) - Updated a bunch of dependencies (unchanged: FastQC, Miniasm, Prokka, Porechop, QUAST) + - Unicycler from 0.4.4 to 0.4.8 + - Kraken2 from 2.0.9beta to 2.1.1 + - MultiQC from 1.9 to 1.10.1 + - PYCOQC from 2.5.0.23 to 2.5.2 + - Samtools from 1.11 to 1.13 + - Canu from 2.0 to 2.1.1-2 + - dfast from 1.2.10 to 1.2.14 + - Medaka from 1.1.2 to 1.4.3-0 + - Minimap 2 from 2.17 to 2.21 + - Nanoplot from 1.32.1 to 1.38.0 + - Nanopolish from 0.13.2 to 0.13.2-5 + - Racon from 1.4.13 to 1.4.20-1 + - Skewer from 0.2.2 to 0.2.2-3 ### `Deprecated` @@ -96,48 +97,48 @@ This version merges the nf-core template update v2.9. It also updates modules or This is basically a maintenance update that includes template updates, fixed environments and some minor bugfixes. -* Merged in nf-core/tools template v 1.10.2 -* Updated dependencies - * fastqc=0.11.8, 0.11.9 - * multiqc=1.8, 1.9 - * kraken2=2.0.8_beta, 2.0.9beta - * prokka=1.14.5, 1.14.6 - * nanopolish=0.11.2, 0.13.2 - * parallel=20191122, 20200922 - * racon=1.4.10, 1.4.13 - * canu=1.9, 2.0 - * samtools=1.9, 1.11 - * nanoplot=1.28.1, 1.32.1 - * pycoqc=2.5.0.3, 2.5.0.23 -* Switched out containers for many tools to make DSLv2 transition easier (escape from dependency hell) +- Merged in nf-core/tools template v 1.10.2 +- Updated dependencies + - fastqc=0.11.8, 0.11.9 + - multiqc=1.8, 1.9 + - kraken2=2.0.8_beta, 2.0.9beta + - prokka=1.14.5, 1.14.6 + - nanopolish=0.11.2, 0.13.2 + - parallel=20191122, 20200922 + - racon=1.4.10, 1.4.13 + - canu=1.9, 2.0 + - samtools=1.9, 1.11 + - nanoplot=1.28.1, 1.32.1 + - pycoqc=2.5.0.3, 2.5.0.23 +- Switched out containers for many tools to make DSLv2 transition easier (escape from dependency hell) ## v1.1.0 nf-core/bacass: "Green Aluminium Shark" 2019/12/13 -* Added support for hybrid assembly using Nanopore and Illumina Short Reads -* Added methods for long-read Nanopore data - * Nanopolish, for polishing of Nanopore data with Illumina reads - * Medaka, as alternative assembly polishing method - * PoreChop, for quality trimming of Nanopore data - * Nanoplot, for plotting quality metrics of Nanopore data - * PycoQC, to QC Nanopore data -* Added multiple tools to assemble long-reads - * Miniasm + Racon - * Canu Assembler - * Unicycler in Long read Mode -* Add alternative assembly annotation using DFAST -* Add social preview image +- Added support for hybrid assembly using Nanopore and Illumina Short Reads +- Added methods for long-read Nanopore data + - Nanopolish, for polishing of Nanopore data with Illumina reads + - Medaka, as alternative assembly polishing method + - PoreChop, for quality trimming of Nanopore data + - Nanoplot, for plotting quality metrics of Nanopore data + - PycoQC, to QC Nanopore data +- Added multiple tools to assemble long-reads + - Miniasm + Racon + - Canu Assembler + - Unicycler in Long read Mode +- Add alternative assembly annotation using DFAST +- Add social preview image ### Dependency updates -* Bumped Nextflow Version to 19.10.0 +- Bumped Nextflow Version to 19.10.0 ## Added tools -* DFAST -* PycoQC -* Nanoplot -* PoreChop -* Nanopolish +- DFAST +- PycoQC +- Nanoplot +- PoreChop +- Nanopolish ## v1.0.0 nf-core/bacass: "Green Tin Ant" diff --git a/CITATIONS.md b/CITATIONS.md index be73036b..eb335184 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -13,49 +13,58 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) * [Skewer](https://pubmed.ncbi.nlm.nih.gov/24925680/) - > Jiang H, Lei R, Ding SW, Zhu S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182. PMID: 24925680; PMCID: PMC4074385. + + > Jiang H, Lei R, Ding SW, Zhu S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182. PMID: 24925680; PMCID: PMC4074385. * [Porechop](https://github.com/rrwick/Porechop) * [NanoPlot](https://doi.org/10.1093/bioinformatics/bty149) - > De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018). NanoPack: visualizing and processing long-read sequencing data. Bioinformatics, 34(15), 2666-2669. doi: 10.1093/bioinformatics/bty149. + + > De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018). NanoPack: visualizing and processing long-read sequencing data. Bioinformatics, 34(15), 2666-2669. doi: 10.1093/bioinformatics/bty149. * [pycoQC](https://github.com/tleonardi/pycoQC) * [Unicycler](https://pubmed.ncbi.nlm.nih.gov/28594827/) - > Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017 Jun 8;13(6):e1005595. doi: 10.1371/journal.pcbi.1005595. PMID: 28594827; PMCID: PMC5481147. + + > Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017 Jun 8;13(6):e1005595. doi: 10.1371/journal.pcbi.1005595. PMID: 28594827; PMCID: PMC5481147. * [Miniasm](https://github.com/lh3/miniasm) with [Racon](https://github.com/isovic/racon) * [Canu](https://pubmed.ncbi.nlm.nih.gov/28298431/) - > Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15. PMID: 28298431; PMCID: PMC5411767. + + > Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15. PMID: 28298431; PMCID: PMC5411767. * [QUAST](https://pubmed.ncbi.nlm.nih.gov/23422339/) - > Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. doi: 10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806. + + > Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. doi: 10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806. * [Prokka](https://pubmed.ncbi.nlm.nih.gov/24642063/) - > Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul 15;30(14):2068-9. doi: 10.1093/bioinformatics/btu153. Epub 2014 Mar 18. PMID: 24642063. + + > Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul 15;30(14):2068-9. doi: 10.1093/bioinformatics/btu153. Epub 2014 Mar 18. PMID: 24642063. * [DFAST](https://pubmed.ncbi.nlm.nih.gov/29106469/) - > Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics. 2018 Mar 15;34(6):1037-1039. doi: 10.1093/bioinformatics/btx713. PMID: 29106469; PMCID: PMC5860143. + + > Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics. 2018 Mar 15;34(6):1037-1039. doi: 10.1093/bioinformatics/btx713. PMID: 29106469; PMCID: PMC5860143. * [Medaka](https://github.com/nanoporetech/medaka) * [Nanopolish](https://github.com/jts/nanopolish) * [SAMtools](https://doi.org/10.1093/bioinformatics/btp352) - > Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics , 25(16), 2078–2079. doi: 10.1093/bioinformatics/btp352. + + > Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics , 25(16), 2078–2079. doi: 10.1093/bioinformatics/btp352. * [Kraken2](https://doi.org/10.1186/s13059-019-1891-0) - > Wood, D et al., 2019. Improved metagenomic analysis with Kraken 2. Genome Biology volume 20, Article number: 257. doi: 10.1186/s13059-019-1891-0. + + > Wood, D et al., 2019. Improved metagenomic analysis with Kraken 2. Genome Biology volume 20, Article number: 257. doi: 10.1186/s13059-019-1891-0. * [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924 + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924 ## Data -* [Full-size test data](https://pubmed.ncbi.nlm.nih.gov/32561582/) - > Blackwell N, Bryce C, Straub D, Kappler A, Kleindienst S. Genomic Insights into Two Novel Fe(II)-Oxidizing Zetaproteobacteria Isolates Reveal Lifestyle Adaption to Coastal Marine Sediments. Appl Environ Microbiol. 2020 Aug 18;86(17):e01160-20. doi: 10.1128/AEM.01160-20. PMID: 32561582; PMCID: PMC7440796. +- [Full-size test data](https://pubmed.ncbi.nlm.nih.gov/32561582/) + > Blackwell N, Bryce C, Straub D, Kappler A, Kleindienst S. Genomic Insights into Two Novel Fe(II)-Oxidizing Zetaproteobacteria Isolates Reveal Lifestyle Adaption to Coastal Marine Sediments. Appl Environ Microbiol. 2020 Aug 18;86(17):e01160-20. doi: 10.1128/AEM.01160-20. PMID: 32561582; PMCID: PMC7440796. ## Software packaging/containerisation tools diff --git a/README.md b/README.md index f0322ca2..641f037c 100644 --- a/README.md +++ b/README.md @@ -107,7 +107,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations -If you use nf-core/bacass for your analysis, please cite it using the following doi: [10.5281/zenodo.2669428](https://doi.org/10.5281/zenodo.2669428) +If you use nf-core/bacass for your analysis, please cite it using the following doi: [10.5281/zenodo.2669428](https://doi.org/10.5281/zenodo.2669428) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/assets/test_config_dfast.py b/assets/test_config_dfast.py index 234b0bdc..0dc915ef 100644 --- a/assets/test_config_dfast.py +++ b/assets/test_config_dfast.py @@ -18,17 +18,15 @@ class Config: # Otherwise, sequences will be renamed as 'Sequence001, Sequence002, ...'. # If 'sort_by_length' is set to True, sequences will be sorted so that longer sequences come first. # In a draft genome, sequences shorter than 'minimum_length' will be eliminated. - "complete": False, - "use_original_name": False, # If set to True, the first word in the Fasta header line will be used as a sequence name. + "use_original_name": False, # If set to True, the first word in the Fasta header line will be used as a sequence name. "sort_by_length": True, - "minimum_length": 200 + "minimum_length": 200, } GENOME_SOURCE_INFORMATION = { # These attributes are reflected in the source feature, # and do not affect the annotation results. - "organism": "", "strain": "", "seq_names": "", @@ -40,17 +38,15 @@ class Config: LOCUS_TAG_SETTINGS = { "locus_tag_prefix": "LOCUS", "step": 10, - "use_separate_tags": True, # If set to `True`, locus_tags are assigned separately according to feature type. + "use_separate_tags": True, # If set to `True`, locus_tags are assigned separately according to feature type. "symbols": {"CDS": "", "rRNA": "r", "tRNA": "t", "tmRNA": "tm"} # "symbols": {"CDS": "", "rRNA": "r", "tRNA": "t", "tmRNA": "tm", "nc_rna": "nc", "misc_rna": "misc"} } FEATURE_ADJUSTMENT = { "remove_partial_features": True, # True: enabled, False: disabled - "remove_overlapping_features": True, # True: enabled, False: disabled "feature_type_priority": ["assembly_gap", "CRISPR", ("tmRNA", "tRNA", "rRNA"), "CDS"], - "merge_cds": False, # True: enabled, False: disabled "tool_type_priority": {"MGA": 0, "Prodigal": 1}, } @@ -60,11 +56,7 @@ class Config: "verbosity": 3 # 1: minimum, 2: standard, 3: rich } - DDBJ_SUBMISSION = { - "enabled": True, - "output_verbosity": 1, - "metadata_file": None - } + DDBJ_SUBMISSION = {"enabled": True, "output_verbosity": 1, "metadata_file": None} GENBANK_SUBMISSION = { "enabled": True, @@ -72,7 +64,6 @@ class Config: "output_verbosity": 1, } - STRUCTURAL_ANNOTATION = [ { # GAP is a Gap Annotation Process that identifies gap regions (N's or n's runs) in the sequence. @@ -81,7 +72,7 @@ class Config: "options": { "len_cutoff": 5, # Gaps shorter than len_cutoff are ignored. "linkage_evidence": "paired-ends", # You can change this as you like. - "gap_type": "within scaffold" # You can change this as you like. + "gap_type": "within scaffold", # You can change this as you like. }, }, { @@ -104,30 +95,24 @@ class Config: # Please insall tRNAscan-SE and put it in your PATH to enable this. "tool_name": "tRNAscan", "enabled": False, - "options": { - "model": "--bact", # --bact, --arch, --organ, --general - "cmd_options": "" - }, + "options": {"model": "--bact", "cmd_options": ""}, # --bact, --arch, --organ, --general }, { # Barrnap for rRNA prediction "tool_name": "Barrnap", - "enabled": False, - "options": { - # Currently, Barrnap will run with default settings. - # You can set parameters such as --reject and --lencutoff to cmd_options. - # "cmd_options": "--reject 0.4 --lencutoff 0.6" - }, + "enabled": False, + "options": { + # Currently, Barrnap will run with default settings. + # You can set parameters such as --reject and --lencutoff to cmd_options. + # "cmd_options": "--reject 0.4 --lencutoff 0.6" + }, }, { # RNAmmer for rRNA prediction. By default, this is disabled. # Please insall RNAmmer and put it in your PATH to enable this. "tool_name": "RNAmmer", "enabled": False, - "options": { - "model": "bac", # arc/bac/euk - "cmd_options": "" - }, + "options": {"model": "bac", "cmd_options": ""}, # arc/bac/euk }, { # CRT for CRISPR detection @@ -151,17 +136,16 @@ class Config: "transl_table": 11, "cmd_options": "", }, - }, + }, ] FUNCTIONAL_ANNOTATION = [ # Fucntional annotation steps will be conducted in the order specified in this list. # You can swithch enabled/disabled, change the order, or add new steps. - { # OrthoSearch (All-vs-all pairwise alignment between each reference genome to assign orthologous genes) # Normally, this should be run before other annotation steps. - # In the default workflow, it is disabled. You can enable this by using the "--references" option. + # In the default workflow, it is disabled. You can enable this by using the "--references" option. "component_name": "OrthoSearch", "enabled": False, "options": { @@ -171,12 +155,11 @@ class Config: "scov_cutoff": 75, "aligner": "ghostx", # ghostx, ghostz, or blastp "aligner_options": {}, # Normally, leave this empty. (Current version does not use this option.) - "references": [ - ] + "references": [], }, }, { - # By default, this is disabled. + # By default, this is disabled. # If you want to add your original databases to be searched in prior to default DB, # set 'enabled' to True and specify 'database' # The database file must be in a DFAST reference format, @@ -254,7 +237,7 @@ class Config: "skipAnnotatedFeatures": False, "evalue_cutoff": 1e-6, "db_name": "", # eg 'Pfam', - "database": "" # eg '@@APP_ROOT@@/db/hmm/Pfam-A.hmm' + "database": "", # eg '@@APP_ROOT@@/db/hmm/Pfam-A.hmm' }, }, { @@ -280,5 +263,4 @@ class Config: "rpsbproc_data": "@@APP_ROOT@@/bin/common/rpsbproc_data", # Do not change this. }, }, - ] diff --git a/docs/output.md b/docs/output.md index d5f221c9..2f5423e1 100644 --- a/docs/output.md +++ b/docs/output.md @@ -10,18 +10,18 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -* [Quality trimming and QC](#quality-trimming-and-qc) - * [Short Read Trimming](#short-read-trimming) - * [Short Read RAW QC](#short-read-raw-qc) - * [Long Read Trimming](#long-read-trimming) - * [Long Read RAW QC](#long-read-raw-qc) -* [Taxonomic classification](#taxonomic-classification) -* [Assembly Output](#assembly-output) - * [Polished assemblies](#polished-assemblies) -* [Assembly QC with QUAST](#assembly-qc-with-quast) -* [Annotation](#annotation) -* [Report](#report) -* [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution +- [Quality trimming and QC](#quality-trimming-and-qc) + - [Short Read Trimming](#short-read-trimming) + - [Short Read RAW QC](#short-read-raw-qc) + - [Long Read Trimming](#long-read-trimming) + - [Long Read RAW QC](#long-read-raw-qc) +- [Taxonomic classification](#taxonomic-classification) +- [Assembly Output](#assembly-output) + - [Polished assemblies](#polished-assemblies) +- [Assembly QC with QUAST](#assembly-qc-with-quast) +- [Annotation](#annotation) +- [Report](#report) +- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ## Quality trimming and QC @@ -33,8 +33,8 @@ combines reads coming from multiple sequencing runs.
    Output files -* `trimming/shortreads/` - * `*.fastp.fastq.gz`: The trimmed/modified/unmerged fastq reads +- `trimming/shortreads/` + - `*.fastp.fastq.gz`: The trimmed/modified/unmerged fastq reads
    @@ -47,9 +47,9 @@ combines reads coming from multiple sequencing runs.
    Output files -* `FastQC/` - * `*.html`: FastQC report containing quality metrics. - * `*.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. +- `FastQC/` + - `*.html`: FastQC report containing quality metrics. + - `*.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. ![FastQC report](images/fastqc.png) @@ -62,9 +62,9 @@ This step performs long read trimming on Nanopore input (if provided).
    Output files -* `trimming/longreads/` - * `*.fastq.gz`: The trimmed FASTQ file - * `*.log*`: Log file +- `trimming/longreads/` + - `*.fastq.gz`: The trimmed FASTQ file + - `*.log*`: Log file
    @@ -77,11 +77,11 @@ Please refer to the documentation of [NanoPlot](https://github.com/wdecoster/Nan
    Output files -* `QC_Longreads/NanoPlot`: Various plots in HTML and PNG format +- `QC_Longreads/NanoPlot`: Various plots in HTML and PNG format -* `QC_Longreads/PycoQC` - * `{sample_id}_pycoqc.html`: QC report in HTML format - * `{sample_id}_pycoqc.json`: QC report in JSON format +- `QC_Longreads/PycoQC` + - `{sample_id}_pycoqc.html`: QC report in HTML format + - `{sample_id}_pycoqc.json`: QC report in JSON format Example plot from Nanoplot: @@ -99,9 +99,9 @@ multiple species. If you like to visualize the report, try
    Output files -* `Kraken2/` - * `{sample}.kraken2.report.txt`: Classification of short reads in the Kraken(1) report format. - * `{sample}_longreads.kraken2.report.txt`: Classification of long reads in the Kraken(1) report format. +- `Kraken2/` + - `{sample}.kraken2.report.txt`: Classification of short reads in the Kraken(1) report format. + - `{sample}_longreads.kraken2.report.txt`: Classification of long reads in the Kraken(1) report format. See [webpage](http://ccb.jhu.edu/software/kraken/MANUAL.html#sample-reports) for more details. @@ -119,22 +119,22 @@ Unicycler is a pipeline on its own, which at least for Illumina reads mainly act
    Output files -* `Unicycler/` - * `{sample}.scaffolds.fa`: Final assembly in fasta format - * `{sample}.assembly.gfa`: Final assembly in Graphical Fragment Assembly (GFA) format - * `{sample}.unicycler.log`: Log file summarizing steps and intermediate results on the Unicycler execution +- `Unicycler/` + - `{sample}.scaffolds.fa`: Final assembly in fasta format + - `{sample}.assembly.gfa`: Final assembly in Graphical Fragment Assembly (GFA) format + - `{sample}.unicycler.log`: Log file summarizing steps and intermediate results on the Unicycler execution Check out the [Unicycler documentation](https://github.com/rrwick/Unicycler) for more information on Unicycler output. -* `Canu/` - * `{sample}.contigs.fasta.gz`: Final assembly in fasta format - * `{sample}.report`: Log file summarizing steps and intermediate results +- `Canu/` + - `{sample}.contigs.fasta.gz`: Final assembly in fasta format + - `{sample}.report`: Log file summarizing steps and intermediate results Check out the [Canu documentation](https://canu.readthedocs.io/en/latest/index.html) for more information on Canu output. -* `Miniasm/` - * `{sample}.fasta.gz`: Assembly in Fasta format - * `{sample}_assembly_consensus.fasta.gz`: Consensus assembly in fasta format (polished by Racon) +- `Miniasm/` + - `{sample}.fasta.gz`: Assembly in Fasta format + - `{sample}_assembly_consensus.fasta.gz`: Consensus assembly in fasta format (polished by Racon) Check out the [Miniasm documentation](https://github.com/lh3/miniasm) for more information on Miniasm output. @@ -147,15 +147,16 @@ Long reads assemblies can be polished using [Medaka](https://github.com/nanopore
    Output files -* `Medaka/{sample_id}_polished_genome.fa` - * `*_polished_genome.fa`: Polished consensus assembly in fasta format - * `calls_to_draft.bam`: Alignment in bam format - * `calls_to_draft.bam.bai`: Index of alignment - * `consensus.fasta.gaps_in_draft_coords.bed` - * `consensus_probs.hdf` +- `Medaka/{sample_id}_polished_genome.fa` -* `Nanopolish/` - * `polished_genome.fa`: Polished consensus assembly in fasta format + - `*_polished_genome.fa`: Polished consensus assembly in fasta format + - `calls_to_draft.bam`: Alignment in bam format + - `calls_to_draft.bam.bai`: Index of alignment + - `consensus.fasta.gaps_in_draft_coords.bed` + - `consensus_probs.hdf` + +- `Nanopolish/` + - `polished_genome.fa`: Polished consensus assembly in fasta format
    @@ -166,12 +167,12 @@ The assembly QC is performed with [QUAST](http://quast.sourceforge.net/quast) fo
    Output files -* `QUAST` - * `report.tsv`: QUAST's report in text format -* `QUAST/report` - * `icarus.html`: QUAST's contig browser as HTML - * `report.html`: QUAST assembly QC as HTML report - * `report.pdf`: QUAST assembly QC as pdf +- `QUAST` + - `report.tsv`: QUAST's report in text format +- `QUAST/report` + - `icarus.html`: QUAST's contig browser as HTML + - `report.html`: QUAST assembly QC as HTML report + - `report.pdf`: QUAST assembly QC as pdf ![QUAST QC](images/quast.png) @@ -186,19 +187,19 @@ By default, the assembly is annotated with [Prokka](https://github.com/tseemann/
    Output files -* `Prokka/{sample_id}/` - * `{sample_id}.gff`: Annotation in gff format - * `{sample_id}.txt`: Annotation in text format - * `{sample_id}.faa`: Protein sequences in fasta format +- `Prokka/{sample_id}/` + - `{sample_id}.gff`: Annotation in gff format + - `{sample_id}.txt`: Annotation in text format + - `{sample_id}.faa`: Protein sequences in fasta format See [Prokka's documentation](https://github.com/tseemann/prokka#output-files) for a full description of all output files. ![Prokka annotation](images/prokka.png) -* `DFAST/{sample_id}_results/` - * `genome.gff`: Annotation in gff format - * `statistics.txt`: Annotation statistics in text format - * `protein.faa`: Protein sequences in fasta format +- `DFAST/{sample_id}_results/` + - `genome.gff`: Annotation in gff format + - `statistics.txt`: Annotation statistics in text format + - `protein.faa`: Protein sequences in fasta format
    diff --git a/docs/usage.md b/docs/usage.md index f2493e49..e35d36dd 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -27,13 +27,13 @@ shortNlong ./data/S1_R1.fastq.gz ./data/S1_R2.fastq.gz ./data/S1_long_f > **NB:** `./data/FAST5` points at a folder containing all (i.e. one or mutiple) fast5 files that correspond to the long reads. `NA` indicates that the file is missing. -| Column | Description | -|-|-| -| `sample` | Custom sample name. May not contain spaces. | -| `R1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". `NA` indicates that the file is missing. | -| `R2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". `NA` indicates that the file is missing. | -| `LongFastQ` | Full path to FastQ file for ONT long reads. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". `NA` indicates that the file is missing. | -| `Fast5` | Full path to a folder containing Fast5 file(s) for ONT long reads. `NA` indicates that there are no Fast5 files available. | +| Column | Description | +| ------------ | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Custom sample name. May not contain spaces. | +| `R1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". `NA` indicates that the file is missing. | +| `R2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". `NA` indicates that the file is missing. | +| `LongFastQ` | Full path to FastQ file for ONT long reads. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". `NA` indicates that the file is missing. | +| `Fast5` | Full path to a folder containing Fast5 file(s) for ONT long reads. `NA` indicates that there are no Fast5 files available. | | `GenomeSize` | Expected genome size. For example, `2.8m` means 2.8 million basepairs genome size expected. This is only used by Canu assembler. `NA` indicates that this value is unknown. | An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. diff --git a/nextflow_schema.json b/nextflow_schema.json index fe2754ce..119f5403 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -52,14 +52,8 @@ "type": "boolean", "description": "save all merged reads to the a file ending in `*.merged.fastq.gz`" }, - "skip_fastqc": { - "type": "boolean", - "description": "Skip FastQC" - }, - "skip_fastp": { - "type": "boolean", - "description": "Skip FastP" - } + "skip_fastqc": { "type": "boolean", "description": "Skip FastQC" }, + "skip_fastp": { "type": "boolean", "description": "Skip FastP" } } }, "contamination_screening": { @@ -183,10 +177,7 @@ "fa_icon": "fas fa-forward", "description": "Skip polishing the long-read assembly with fast5 input. Will not affect short/hybrid assemblies." }, - "skip_multiqc": { - "type": "boolean", - "description": "Skip MultiQC" - } + "skip_multiqc": { "type": "boolean", "description": "Skip MultiQC" } } }, "institutional_config_options": { @@ -396,35 +387,15 @@ } }, "allOf": [ - { - "$ref": "#/definitions/input_output_options" - }, - { - "$ref": "#/definitions/qc_and_trim" - }, - { - "$ref": "#/definitions/contamination_screening" - }, - { - "$ref": "#/definitions/assembly_parameters" - }, - { - "$ref": "#/definitions/assembly_polishing" - }, - { - "$ref": "#/definitions/annotation" - }, - { - "$ref": "#/definitions/skipping_options" - }, - { - "$ref": "#/definitions/institutional_config_options" - }, - { - "$ref": "#/definitions/max_job_request_options" - }, - { - "$ref": "#/definitions/generic_options" - } + { "$ref": "#/definitions/input_output_options" }, + { "$ref": "#/definitions/qc_and_trim" }, + { "$ref": "#/definitions/contamination_screening" }, + { "$ref": "#/definitions/assembly_parameters" }, + { "$ref": "#/definitions/assembly_polishing" }, + { "$ref": "#/definitions/annotation" }, + { "$ref": "#/definitions/skipping_options" }, + { "$ref": "#/definitions/institutional_config_options" }, + { "$ref": "#/definitions/max_job_request_options" }, + { "$ref": "#/definitions/generic_options" } ] } From 686279d0047aac3bb3fbe9a5502e9eab846e8067 Mon Sep 17 00:00:00 2001 From: Dani VM Date: Mon, 11 Sep 2023 18:34:04 +0200 Subject: [PATCH 14/21] fix editorConfig --- .github/workflows/ci.yml | 2 +- conf/modules.config | 2 +- conf/test_dfast.config | 4 ++-- modules/local/dfast.nf | 1 - modules/local/kraken2_db_preparation.nf | 2 +- modules/local/medaka.nf | 2 +- 6 files changed, 6 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9eab305d..02204b23 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -47,7 +47,7 @@ jobs: if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/bacass') }} runs-on: ubuntu-latest env: - NXF_VER: '21.04.0' + NXF_VER: '23.04.0' NXF_ANSI_LOG: false strategy: matrix: diff --git a/conf/modules.config b/conf/modules.config index 63961459..aa0d621d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -142,7 +142,7 @@ process { if (filename.equals('versions.yml')) { null } else { - "${filename.replaceFirst('\\..+$', '')}_longreads${filename.substring(filename.lastIndexOf('.'))}" + "${filename.replaceFirst('\\..+$', '')}_longreads${filename.substring(filename.lastIndexOf('.'))}" } } ] diff --git a/conf/test_dfast.config b/conf/test_dfast.config index 756554d9..2ab10265 100644 --- a/conf/test_dfast.config +++ b/conf/test_dfast.config @@ -27,5 +27,5 @@ params { annotation_tool = 'dfast' assembly_type = 'short' skip_pycoqc = true - skip_kraken2 = true -} \ No newline at end of file + skip_kraken2 = true +} diff --git a/modules/local/dfast.nf b/modules/local/dfast.nf index 001518fb..db7be3da 100644 --- a/modules/local/dfast.nf +++ b/modules/local/dfast.nf @@ -22,7 +22,6 @@ process DFAST { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - """ dfast_file_downloader.py \\ $args \\ diff --git a/modules/local/kraken2_db_preparation.nf b/modules/local/kraken2_db_preparation.nf index aa10cde4..bfcb945d 100644 --- a/modules/local/kraken2_db_preparation.nf +++ b/modules/local/kraken2_db_preparation.nf @@ -3,7 +3,7 @@ process KRAKEN2_DB_PREPARATION { label 'process_low' conda 'conda-forge::sed=4.7' - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : 'biocontainers/biocontainers:v1.2.0_cv1' }" diff --git a/modules/local/medaka.nf b/modules/local/medaka.nf index 0d711a6c..e57666a8 100644 --- a/modules/local/medaka.nf +++ b/modules/local/medaka.nf @@ -35,7 +35,7 @@ process MEDAKA { -d ${ assembly_bgzip_out ?: assembly } \ -o "${prefix}_polished_genome.fa" \ -t $task.cpus - + cat <<-END_VERSIONS > versions.yml "${task.process}": medaka: \$( medaka --version 2>&1 | sed 's/medaka //g' ) From 3858449e4c94e277bdda175360db30a2fb43b474 Mon Sep 17 00:00:00 2001 From: Dani VM Date: Mon, 11 Sep 2023 18:39:23 +0200 Subject: [PATCH 15/21] fix prettier typo --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 02204b23..2a9d3723 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -47,7 +47,7 @@ jobs: if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/bacass') }} runs-on: ubuntu-latest env: - NXF_VER: '23.04.0' + NXF_VER: "23.04.0" NXF_ANSI_LOG: false strategy: matrix: From a1fc98abf6ac030bd07022062a897a9601969381 Mon Sep 17 00:00:00 2001 From: Dani VM Date: Tue, 12 Sep 2023 15:12:56 +0200 Subject: [PATCH 16/21] fix CI test --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2a9d3723..bf037552 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -39,7 +39,7 @@ jobs: # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir results profiles: name: Run workflow profile @@ -65,4 +65,4 @@ jobs: sudo mv nextflow /usr/local/bin/ - name: Run pipeline with ${{ matrix.profile }} test profile run: | - nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir results From 61d4761271eb9b4cf14bcb3f2be449cf834ea556 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 13 Sep 2023 17:28:03 +0200 Subject: [PATCH 17/21] Fix missing snippet while merging conflicts --- modules/local/kraken2_db_preparation.nf | 2 +- nextflow.config | 32 +++++++++++++++++++++++-- 2 files changed, 31 insertions(+), 3 deletions(-) diff --git a/modules/local/kraken2_db_preparation.nf b/modules/local/kraken2_db_preparation.nf index bfcb945d..d2af01b6 100644 --- a/modules/local/kraken2_db_preparation.nf +++ b/modules/local/kraken2_db_preparation.nf @@ -5,7 +5,7 @@ process KRAKEN2_DB_PREPARATION { conda 'conda-forge::sed=4.7' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : - 'biocontainers/biocontainers:v1.2.0_cv1' }" + 'docker.io/biocontainers/biocontainers:v1.2.0_cv1' }" input: path db diff --git a/nextflow.config b/nextflow.config index f60a4dc6..cc5c6a33 100644 --- a/nextflow.config +++ b/nextflow.config @@ -15,7 +15,7 @@ params { // QC and trimming options save_trimmed_fail = false save_merged = false - + // Contamination_screening kraken2db = "" @@ -70,7 +70,7 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - + // Max resource options // Defaults only, expecting to be overwritten @@ -177,6 +177,21 @@ profiles { singularity.enabled = false podman.enabled = false shifter.enabled = false + apptainer.enabled = false + } + apptainer { + apptainer.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + gitpod { + executor.name = 'local' + executor.cpus = 16 + executor.memory = 60.GB } test { includeConfig 'conf/test.config' } test_dfast { includeConfig 'conf/test_dfast.config' } @@ -186,6 +201,19 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Nextflow plugins +plugins { + id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. From c9dbfcc25f801722318939eab01377b5c35d45c2 Mon Sep 17 00:00:00 2001 From: Dani VM Date: Tue, 19 Sep 2023 09:18:38 +0200 Subject: [PATCH 18/21] make patch to Nanoplot --- conf/modules.config | 3 +- modules.json | 6 ++ .../nanoplot/main.nf} | 3 +- modules/nf-core/nanoplot/meta.yml | 59 +++++++++++++++++++ modules/nf-core/nanoplot/nanoplot.diff | 15 +++++ 5 files changed, 82 insertions(+), 4 deletions(-) rename modules/{local/nanoplot_custom.nf => nf-core/nanoplot/main.nf} (91%) create mode 100644 modules/nf-core/nanoplot/meta.yml create mode 100644 modules/nf-core/nanoplot/nanoplot.diff diff --git a/conf/modules.config b/conf/modules.config index aa0d621d..4403db65 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -10,11 +10,10 @@ ---------------------------------------------------------------------------------------- */ -// TODO: Think about segregating modules.config in modules_shortreads.config and modules_longreads.config files // Let modules.config to store module configurations that share both shortreads and longreads process { - withName: 'NANOPLOT_CUSTOM' { + withName: 'NANOPLOT' { ext.args = '' publishDir = [ path: { "${params.outdir}/QC_longreads/NanoPlot" }, diff --git a/modules.json b/modules.json index 514171f2..b7e35f46 100644 --- a/modules.json +++ b/modules.json @@ -50,6 +50,12 @@ "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", "installed_by": ["modules"] }, + "nanoplot": { + "branch": "master", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"], + "patch": "modules/nf-core/nanoplot/nanoplot.diff" + }, "porechop/porechop": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", diff --git a/modules/local/nanoplot_custom.nf b/modules/nf-core/nanoplot/main.nf similarity index 91% rename from modules/local/nanoplot_custom.nf rename to modules/nf-core/nanoplot/main.nf index 6cdec625..e276cc89 100644 --- a/modules/local/nanoplot_custom.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -1,5 +1,4 @@ -// Imported from nf-core/modules/nanoplot but allow it to work with *.fq.gz files too. -process NANOPLOT_CUSTOM { +process NANOPLOT { tag "$meta.id" label 'process_low' diff --git a/modules/nf-core/nanoplot/meta.yml b/modules/nf-core/nanoplot/meta.yml new file mode 100644 index 00000000..28c8c2d3 --- /dev/null +++ b/modules/nf-core/nanoplot/meta.yml @@ -0,0 +1,59 @@ +name: nanoplot +description: Run NanoPlot on nanopore-sequenced reads +keywords: + - quality control + - qc + - fastq + - sequencing summary + - nanopore +tools: + - nanoplot: + description: | + NanoPlot is a tool for ploting long-read sequencing data and + alignment. + homepage: http://nanoplot.bioinf.be + documentation: https://github.com/wdecoster/NanoPlot + licence: ["GPL-3.0-or-later"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: | + List of input basecalled-FastQ files. + - summary_txt: + type: file + description: | + List of sequencing_summary.txt files from running basecalling. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - html: + type: file + description: NanoPlot report + pattern: "*{.html}" + - png: + type: file + description: Plots generated by NanoPlot + pattern: "*{.png}" + - txt: + type: file + description: Stats from NanoPlot + pattern: "*{.txt}" + - log: + type: file + description: log file of NanoPlot run + pattern: "*{.log}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@yuukiiwa" diff --git a/modules/nf-core/nanoplot/nanoplot.diff b/modules/nf-core/nanoplot/nanoplot.diff new file mode 100644 index 00000000..dc4cc687 --- /dev/null +++ b/modules/nf-core/nanoplot/nanoplot.diff @@ -0,0 +1,15 @@ +Changes in module 'nf-core/nanoplot' +--- modules/nf-core/nanoplot/main.nf ++++ modules/nf-core/nanoplot/main.nf +@@ -22,8 +22,7 @@ + + script: + def args = task.ext.args ?: '' +- def input_file = ("$ontfile".endsWith(".fastq.gz")) ? "--fastq ${ontfile}" : +- ("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : '' ++ def input_file = ("$ontfile".endsWith(".fastq.gz") || "$ontfile".endsWith(".fq.gz")) ? "--fastq ${ontfile}" : ("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : '' + """ + NanoPlot \\ + $args \\ + +************************************************************ From 715b86aeaba0699c49575dd5db82269576303213 Mon Sep 17 00:00:00 2001 From: Dani VM Date: Tue, 19 Sep 2023 16:58:46 +0200 Subject: [PATCH 19/21] Apply suggestios from code reviewer --- .nf-core.yml | 3 + CHANGELOG.md | 50 ++- CITATIONS.md | 34 +- README.md | 19 +- assets/{samplesheet.csv => samplesheet.tsv} | 0 bin/check_samplesheet.py | 259 ------------ conf/igenomes.config | 440 -------------------- docs/output.md | 35 +- docs/usage.md | 7 +- modules/local/pycoqc.nf | 5 +- modules/local/samplesheet_check.nf | 31 -- nextflow.config | 108 +++-- workflows/bacass.nf | 22 +- 13 files changed, 146 insertions(+), 867 deletions(-) rename assets/{samplesheet.csv => samplesheet.tsv} (100%) delete mode 100755 bin/check_samplesheet.py delete mode 100644 conf/igenomes.config delete mode 100644 modules/local/samplesheet_check.nf diff --git a/.nf-core.yml b/.nf-core.yml index 3805dc81..778ae193 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1 +1,4 @@ repository_type: pipeline +lint: + files_exist: + - conf/igenomes.config diff --git a/CHANGELOG.md b/CHANGELOG.md index 3bccdc38..3e70f466 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,13 +3,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.0.1dev nf-core/bacass: "Navy Steel Swordfish" - 2023/09/11 +## v2.1.0dev nf-core/bacass: "Navy Steel Swordfish" - 2023/09/11 This version merges the nf-core template update v2.9. It also updates modules or dependencies to make them work with the new template. ### `Changed` -- [#84](https://github.com/nf-core/bacass/pull/84) & [#85](https://github.com/nf-core/bacass/issues/85) - Update nf-core/bacass to the new nf-core 2.0 `TEMPLATE`. +- [#86](https://github.com/nf-core/bacass/pull/86) - Update nf-core/bacass to the new nf-core 2.9 `TEMPLATE`. - [#61](https://github.com/nf-core/bacass/issues/61) - Update local/modules to nf-core/modules (detailed below). @@ -26,38 +26,44 @@ This version merges the nf-core template update v2.9. It also updates modules or ### `Dependencies` -- [#61](https://github.com/nf-core/bacass/issues/61) - Update a bunch of local/modules to nf-core/modules plus version update. +- [#61](https://github.com/nf-core/bacass/issues/61) - Update local/modules to nf-core/modules plus version update. - - Canu (v2.1.1 → v2.2) - - Minimap2 (v2.21 → v2.24) - - Miniasm - - Racon +| Tool | Previous version | New version | +| ------ | ---------------- | ----------- | +| Canu | 2.1.1 | 2.2 | +| Minimap2 | 2.21 | 2.2 | +| Miniasm | 0.3 | - | +| Racon | 1.4.20-1 | - | -- [#84](https://github.com/nf-core/bacass/pull/84) Update already nf-core modules +- Update already nf-core modules - - Fastqc - - Samtools (v1.13 → v1.17) - - Kraken2 (v2.1.1 → v2.1.2) - - Quast (v5.0.2 → 5.2.0) - - Prokka - - Multiqc (v1.10.1 → v1.15) +| Tool | Previous version | New version | +| ------ | ---------------- | ----------- | +| Fastqc | 0.11.9 | - | +| Samtools | 1.13 | 2.1.2 | +| Kraken2 | 2.1.1 | 2.1.2 | +| Quast | 5.0.2 | 5.2.0 | +| Prokka | 1.14.6 | - | +| Multiqc | 1.10.1 | 1.15 | - Refactor `local/modules` making them follow nf-core v2.9 structure/fashion. - - Dfast - - Medaka - - Nanoplot (v1.38.0 → v1.41.6) - - Nanopolish (v0.13.2-5 → 0.14.0) - - Pycoqc - - Unicycler +| Tool | Previous version | New version | +| ------ | ---------------- | ----------- | +| Dfast | 1.2.14 | - | +| Medaka | 1.4.3-0 | - | +| Nanoplot | 1.38.0 | 1.41.6 | + | Nanopolish | 0.13.2-5 | 0.14.0 | + | Pycoqc | 2.5.2 | - | + | Unicycler | 0.4.8 | - | + ### `Deprecated` -- [#61](https://github.com/nf-core/bacass/issues/61) - Replace depecated modules with nf-core/modules. +- [#86](https://github.com/nf-core/bacass/pull/86) Replace depecated modules with nf-core/modules. - Replace `local/get_software_versions.nf` with `nf-core/custom/dumpsoftwareversions.nf` - Replace `local/skewer` by `nf-core/fastp` and wrap fastqc plus fastp into `subworkflows/nf-core/fastq_trim_fastp_fastqc` - - Replace `local/nanoplot` by local/nanoplot_custom (using as template nf-core/nanoplot). ## v2.0.0 nf-core/bacass: "Navy Steel Swordfish" 2021/08/27 diff --git a/CITATIONS.md b/CITATIONS.md index eb335184..b5969616 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,53 +12,55 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -* [Skewer](https://pubmed.ncbi.nlm.nih.gov/24925680/) +- [FastP](https://github.com/OpenGene/fastp) - > Jiang H, Lei R, Ding SW, Zhu S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182. PMID: 24925680; PMCID: PMC4074385. + > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PMID: 30423086; PMCID: PMC6129281. -* [Porechop](https://github.com/rrwick/Porechop) +- [Porechop](https://github.com/rrwick/Porechop) -* [NanoPlot](https://doi.org/10.1093/bioinformatics/bty149) +- [NanoPlot](https://doi.org/10.1093/bioinformatics/bty149) > De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018). NanoPack: visualizing and processing long-read sequencing data. Bioinformatics, 34(15), 2666-2669. doi: 10.1093/bioinformatics/bty149. -* [pycoQC](https://github.com/tleonardi/pycoQC) +- [pycoQC](https://github.com/tleonardi/pycoQC) -* [Unicycler](https://pubmed.ncbi.nlm.nih.gov/28594827/) +- [Unicycler](https://pubmed.ncbi.nlm.nih.gov/28594827/) > Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017 Jun 8;13(6):e1005595. doi: 10.1371/journal.pcbi.1005595. PMID: 28594827; PMCID: PMC5481147. -* [Miniasm](https://github.com/lh3/miniasm) with [Racon](https://github.com/isovic/racon) +- [Miniasm](https://github.com/lh3/miniasm) with [Racon](https://github.com/isovic/racon) -* [Canu](https://pubmed.ncbi.nlm.nih.gov/28298431/) + > Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics. 2016 Jul 15;32(14):2103-10. doi: 10.1093/bioinformatics/btw152. Epub 2016 Mar 19. PMID: 27153593; PMCID: PMC4937194. + +- [Canu](https://pubmed.ncbi.nlm.nih.gov/28298431/) > Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15. PMID: 28298431; PMCID: PMC5411767. -* [QUAST](https://pubmed.ncbi.nlm.nih.gov/23422339/) +- [QUAST](https://pubmed.ncbi.nlm.nih.gov/23422339/) > Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. doi: 10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806. -* [Prokka](https://pubmed.ncbi.nlm.nih.gov/24642063/) +- [Prokka](https://pubmed.ncbi.nlm.nih.gov/24642063/) > Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul 15;30(14):2068-9. doi: 10.1093/bioinformatics/btu153. Epub 2014 Mar 18. PMID: 24642063. -* [DFAST](https://pubmed.ncbi.nlm.nih.gov/29106469/) +- [DFAST](https://pubmed.ncbi.nlm.nih.gov/29106469/) > Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics. 2018 Mar 15;34(6):1037-1039. doi: 10.1093/bioinformatics/btx713. PMID: 29106469; PMCID: PMC5860143. -* [Medaka](https://github.com/nanoporetech/medaka) +- [Medaka](https://github.com/nanoporetech/medaka) -* [Nanopolish](https://github.com/jts/nanopolish) +- [Nanopolish](https://github.com/jts/nanopolish) -* [SAMtools](https://doi.org/10.1093/bioinformatics/btp352) +- [SAMtools](https://doi.org/10.1093/bioinformatics/btp352) > Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics , 25(16), 2078–2079. doi: 10.1093/bioinformatics/btp352. -* [Kraken2](https://doi.org/10.1186/s13059-019-1891-0) +- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0) > Wood, D et al., 2019. Improved metagenomic analysis with Kraken 2. Genome Biology volume 20, Article number: 257. doi: 10.1186/s13059-019-1891-0. -* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/) +- [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924 ## Data diff --git a/README.md b/README.md index 641f037c..48f0d4a8 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ On release, automated continuous integration tests run the pipeline on a full-si ### Short Read Assembly -This pipeline is primarily for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using [Skewer](https://github.com/relipmoc/skewer) and performs basic sequencing QC using [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, the pipeline performs read assembly using [Unicycler](https://github.com/rrwick/Unicycler). Contamination of the assembly is checked using [Kraken2](https://ccb.jhu.edu/software/kraken2/) to verify sample purity. +This pipeline is primarily for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using [FastP](https://github.com/OpenGene/fastp) and performs basic sequencing QC using [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, the pipeline performs read assembly using [Unicycler](https://github.com/rrwick/Unicycler). Contamination of the assembly is checked using [Kraken2](https://ccb.jhu.edu/software/kraken2/) to verify sample purity. ### Long Read Assembly @@ -52,16 +52,19 @@ In all cases, the assembly is assessed using [QUAST](http://bioinf.spbau.ru/quas First, prepare a samplesheet with your input data that looks as follows: -`samplesheet.csv`: +`samplesheet.tsv`: + +```tsv +ID R1 R2 LongFastQ Fast5 GenomeSize +shortreads ./data/S1_R1.fastq.gz ./data/S1_R2.fastq.gz NA NA NA +longreads NA NA ./data/S1_long_fastq.gz ./data/FAST5 2.8m +shortNlong ./data/S1_R1.fastq.gz ./data/S1_R2.fastq.gz ./data/S1_long_fastq.gz ./data/FAST5 2.8m -```csv -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz ``` Each row represents a fastq file (single-end) or a pair of fastq files (paired end). - Default: Short read assembly with Unicycler, `--kraken2db` can be any [compressed database (`.tar.gz`/`.tgz`)](https://benlangmead.github.io/aws-indexes/k2): +Default: Short read assembly with Unicycler, `--kraken2db` can be any [compressed database (`.tar.gz`/`.tgz`)](https://benlangmead.github.io/aws-indexes/k2): ```console nextflow run nf-core/bacass -profile --input samplesheet.tsv --kraken2db "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz" @@ -78,7 +81,7 @@ Each row represents a fastq file (single-end) or a pair of fastq files (paired e ```bash nextflow run nf-core/bacass \ -profile \ - --input samplesheet.csv \ + --input samplesheet.tsv \ --outdir ``` @@ -97,7 +100,7 @@ For more details about the output files and reports, please refer to the ## Credits -nf-core/bacass was initiated by [Andreas Wilm](https://github.com/andreas-wilm), originally written by [Alex Peltzer](https://github.com/apeltzer) (DSL1) and rewritten by [Daniel Straub](https://github.com/d4straub) (DSL2). +nf-core/bacass was initiated by [Andreas Wilm](https://github.com/andreas-wilm), originally written by [Alex Peltzer](https://github.com/apeltzer) (DSL1), rewritten by [Daniel Straub](https://github.com/d4straub) (DSL2) and maintained by [Daniel Valle-Millares](https://github.com/Daniel-VM). ## Contributions and Support diff --git a/assets/samplesheet.csv b/assets/samplesheet.tsv similarity index 100% rename from assets/samplesheet.csv rename to assets/samplesheet.tsv diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py deleted file mode 100755 index 4a758fe0..00000000 --- a/bin/check_samplesheet.py +++ /dev/null @@ -1,259 +0,0 @@ -#!/usr/bin/env python - - -"""Provide a command line tool to validate and transform tabular samplesheets.""" - - -import argparse -import csv -import logging -import sys -from collections import Counter -from pathlib import Path - -logger = logging.getLogger() - - -class RowChecker: - """ - Define a service that can validate and transform each given row. - - Attributes: - modified (list): A list of dicts, where each dict corresponds to a previously - validated and transformed row. The order of rows is maintained. - - """ - - VALID_FORMATS = ( - ".fq.gz", - ".fastq.gz", - ) - - def __init__( - self, - sample_col="sample", - first_col="fastq_1", - second_col="fastq_2", - single_col="single_end", - **kwargs, - ): - """ - Initialize the row checker with the expected column names. - - Args: - sample_col (str): The name of the column that contains the sample name - (default "sample"). - first_col (str): The name of the column that contains the first (or only) - FASTQ file path (default "fastq_1"). - second_col (str): The name of the column that contains the second (if any) - FASTQ file path (default "fastq_2"). - single_col (str): The name of the new column that will be inserted and - records whether the sample contains single- or paired-end sequencing - reads (default "single_end"). - - """ - super().__init__(**kwargs) - self._sample_col = sample_col - self._first_col = first_col - self._second_col = second_col - self._single_col = single_col - self._seen = set() - self.modified = [] - - def validate_and_transform(self, row): - """ - Perform all validations on the given row and insert the read pairing status. - - Args: - row (dict): A mapping from column headers (keys) to elements of that row - (values). - - """ - self._validate_sample(row) - self._validate_first(row) - self._validate_second(row) - self._validate_pair(row) - self._seen.add((row[self._sample_col], row[self._first_col])) - self.modified.append(row) - - def _validate_sample(self, row): - """Assert that the sample name exists and convert spaces to underscores.""" - if len(row[self._sample_col]) <= 0: - raise AssertionError("Sample input is required.") - # Sanitize samples slightly. - row[self._sample_col] = row[self._sample_col].replace(" ", "_") - - def _validate_first(self, row): - """Assert that the first FASTQ entry is non-empty and has the right format.""" - if len(row[self._first_col]) <= 0: - raise AssertionError("At least the first FASTQ file is required.") - self._validate_fastq_format(row[self._first_col]) - - def _validate_second(self, row): - """Assert that the second FASTQ entry has the right format if it exists.""" - if len(row[self._second_col]) > 0: - self._validate_fastq_format(row[self._second_col]) - - def _validate_pair(self, row): - """Assert that read pairs have the same file extension. Report pair status.""" - if row[self._first_col] and row[self._second_col]: - row[self._single_col] = False - first_col_suffix = Path(row[self._first_col]).suffixes[-2:] - second_col_suffix = Path(row[self._second_col]).suffixes[-2:] - if first_col_suffix != second_col_suffix: - raise AssertionError("FASTQ pairs must have the same file extensions.") - else: - row[self._single_col] = True - - def _validate_fastq_format(self, filename): - """Assert that a given filename has one of the expected FASTQ extensions.""" - if not any(filename.endswith(extension) for extension in self.VALID_FORMATS): - raise AssertionError( - f"The FASTQ file has an unrecognized extension: {filename}\n" - f"It should be one of: {', '.join(self.VALID_FORMATS)}" - ) - - def validate_unique_samples(self): - """ - Assert that the combination of sample name and FASTQ filename is unique. - - In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the - number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment. - - """ - if len(self._seen) != len(self.modified): - raise AssertionError("The pair of sample name and FASTQ must be unique.") - seen = Counter() - for row in self.modified: - sample = row[self._sample_col] - seen[sample] += 1 - row[self._sample_col] = f"{sample}_T{seen[sample]}" - - -def read_head(handle, num_lines=10): - """Read the specified number of lines from the current position in the file.""" - lines = [] - for idx, line in enumerate(handle): - if idx == num_lines: - break - lines.append(line) - return "".join(lines) - - -def sniff_format(handle): - """ - Detect the tabular format. - - Args: - handle (text file): A handle to a `text file`_ object. The read position is - expected to be at the beginning (index 0). - - Returns: - csv.Dialect: The detected tabular format. - - .. _text file: - https://docs.python.org/3/glossary.html#term-text-file - - """ - peek = read_head(handle) - handle.seek(0) - sniffer = csv.Sniffer() - dialect = sniffer.sniff(peek) - return dialect - - -def check_samplesheet(file_in, file_out): - """ - Check that the tabular samplesheet has the structure expected by nf-core pipelines. - - Validate the general shape of the table, expected columns, and each row. Also add - an additional column which records whether one or two FASTQ reads were found. - - Args: - file_in (pathlib.Path): The given tabular samplesheet. The format can be either - CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. - file_out (pathlib.Path): Where the validated and transformed samplesheet should - be created; always in CSV format. - - Example: - This function checks that the samplesheet follows the following structure, - see also the `viral recon samplesheet`_:: - - sample,fastq_1,fastq_2 - SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz - SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz - SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, - - .. _viral recon samplesheet: - https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv - - """ - required_columns = {"sample", "fastq_1", "fastq_2"} - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_in.open(newline="") as in_handle: - reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) - # Validate the existence of the expected header columns. - if not required_columns.issubset(reader.fieldnames): - req_cols = ", ".join(required_columns) - logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.") - sys.exit(1) - # Validate each row. - checker = RowChecker() - for i, row in enumerate(reader): - try: - checker.validate_and_transform(row) - except AssertionError as error: - logger.critical(f"{str(error)} On line {i + 2}.") - sys.exit(1) - checker.validate_unique_samples() - header = list(reader.fieldnames) - header.insert(1, "single_end") - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_out.open(mode="w", newline="") as out_handle: - writer = csv.DictWriter(out_handle, header, delimiter=",") - writer.writeheader() - for row in checker.modified: - writer.writerow(row) - - -def parse_args(argv=None): - """Define and immediately parse command line arguments.""" - parser = argparse.ArgumentParser( - description="Validate and transform a tabular samplesheet.", - epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", - ) - parser.add_argument( - "file_in", - metavar="FILE_IN", - type=Path, - help="Tabular input samplesheet in CSV or TSV format.", - ) - parser.add_argument( - "file_out", - metavar="FILE_OUT", - type=Path, - help="Transformed output samplesheet in CSV format.", - ) - parser.add_argument( - "-l", - "--log-level", - help="The desired log level (default WARNING).", - choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), - default="WARNING", - ) - return parser.parse_args(argv) - - -def main(argv=None): - """Coordinate argument parsing and program execution.""" - args = parse_args(argv) - logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") - if not args.file_in.is_file(): - logger.error(f"The given input file {args.file_in} was not found!") - sys.exit(2) - args.file_out.parent.mkdir(parents=True, exist_ok=True) - check_samplesheet(args.file_in, args.file_out) - - -if __name__ == "__main__": - sys.exit(main()) diff --git a/conf/igenomes.config b/conf/igenomes.config deleted file mode 100644 index 3f114377..00000000 --- a/conf/igenomes.config +++ /dev/null @@ -1,440 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for iGenomes paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines reference genomes using iGenome paths. - Can be used by any config that customises the base path using: - $params.igenomes_base / --igenomes_base ----------------------------------------------------------------------------------------- -*/ - -params { - // illumina iGenomes reference file paths - genomes { - 'GRCh37' { - fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" - } - 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'CHM13' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" - bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" - gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" - mito_name = "chrM" - } - 'GRCm38' { - fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" - } - 'TAIR10' { - fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" - mito_name = "Mt" - } - 'EB2' { - fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" - } - 'UMD3.1' { - fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" - mito_name = "MT" - } - 'WBcel235' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" - mito_name = "MtDNA" - macs_gsize = "9e7" - } - 'CanFam3.1' { - fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" - mito_name = "MT" - } - 'GRCz10' { - fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'BDGP6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" - mito_name = "M" - macs_gsize = "1.2e8" - } - 'EquCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" - mito_name = "MT" - } - 'EB1' { - fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" - } - 'Galgal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Gm01' { - fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" - } - 'Mmul_1' { - fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" - mito_name = "MT" - } - 'IRGSP-1.0' { - fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'CHIMP2.1.4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" - mito_name = "MT" - } - 'Rnor_5.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Rnor_6.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'R64-1-1' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" - mito_name = "MT" - macs_gsize = "1.2e7" - } - 'EF2' { - fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.21e7" - } - 'Sbi1' { - fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" - } - 'Sscrofa10.2' { - fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" - mito_name = "MT" - } - 'AGPv3' { - fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'hg38' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'hg19' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" - } - 'mm10' { - fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" - } - 'bosTau8' { - fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'ce10' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "9e7" - } - 'canFam3' { - fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" - mito_name = "chrM" - } - 'danRer10' { - fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.37e9" - } - 'dm6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.2e8" - } - 'equCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" - mito_name = "chrM" - } - 'galGal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" - mito_name = "chrM" - } - 'panTro4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" - mito_name = "chrM" - } - 'rn6' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'sacCer3' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" - readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.2e7" - } - 'susScr3' { - fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" - mito_name = "chrM" - } - } -} diff --git a/docs/output.md b/docs/output.md index 2f5423e1..4a6a5939 100644 --- a/docs/output.md +++ b/docs/output.md @@ -80,8 +80,8 @@ Please refer to the documentation of [NanoPlot](https://github.com/wdecoster/Nan - `QC_Longreads/NanoPlot`: Various plots in HTML and PNG format - `QC_Longreads/PycoQC` - - `{sample_id}_pycoqc.html`: QC report in HTML format - - `{sample_id}_pycoqc.json`: QC report in JSON format + - `*_pycoqc.html`: QC report in HTML format + - `*_pycoqc.json`: QC report in JSON format Example plot from Nanoplot: @@ -100,8 +100,8 @@ multiple species. If you like to visualize the report, try Output files - `Kraken2/` - - `{sample}.kraken2.report.txt`: Classification of short reads in the Kraken(1) report format. - - `{sample}_longreads.kraken2.report.txt`: Classification of long reads in the Kraken(1) report format. + - `*.kraken2.report.txt`: Classification of short reads in the Kraken(1) report format. + - `*_longreads.kraken2.report.txt`: Classification of long reads in the Kraken(1) report format. See [webpage](http://ccb.jhu.edu/software/kraken/MANUAL.html#sample-reports) for more details. @@ -120,21 +120,21 @@ Unicycler is a pipeline on its own, which at least for Illumina reads mainly act Output files - `Unicycler/` - - `{sample}.scaffolds.fa`: Final assembly in fasta format - - `{sample}.assembly.gfa`: Final assembly in Graphical Fragment Assembly (GFA) format - - `{sample}.unicycler.log`: Log file summarizing steps and intermediate results on the Unicycler execution + - `*.scaffolds.fa`: Final assembly in fasta format + - `*.assembly.gfa`: Final assembly in Graphical Fragment Assembly (GFA) format + - `*.unicycler.log`: Log file summarizing steps and intermediate results on the Unicycler execution Check out the [Unicycler documentation](https://github.com/rrwick/Unicycler) for more information on Unicycler output. - `Canu/` - - `{sample}.contigs.fasta.gz`: Final assembly in fasta format - - `{sample}.report`: Log file summarizing steps and intermediate results + - `*.contigs.fasta.gz`: Final assembly in fasta format + - `*.report`: Log file summarizing steps and intermediate results Check out the [Canu documentation](https://canu.readthedocs.io/en/latest/index.html) for more information on Canu output. - `Miniasm/` - - `{sample}.fasta.gz`: Assembly in Fasta format - - `{sample}_assembly_consensus.fasta.gz`: Consensus assembly in fasta format (polished by Racon) + - `*.fasta.gz`: Assembly in Fasta format + - `*_assembly_consensus.fasta.gz`: Consensus assembly in fasta format (polished by Racon) Check out the [Miniasm documentation](https://github.com/lh3/miniasm) for more information on Miniasm output. @@ -147,7 +147,7 @@ Long reads assemblies can be polished using [Medaka](https://github.com/nanopore
    Output files -- `Medaka/{sample_id}_polished_genome.fa` +- `Medaka/*_polished_genome.fa` - `*_polished_genome.fa`: Polished consensus assembly in fasta format - `calls_to_draft.bam`: Alignment in bam format @@ -187,16 +187,16 @@ By default, the assembly is annotated with [Prokka](https://github.com/tseemann/
    Output files -- `Prokka/{sample_id}/` - - `{sample_id}.gff`: Annotation in gff format - - `{sample_id}.txt`: Annotation in text format - - `{sample_id}.faa`: Protein sequences in fasta format +- `Prokka/{ID}/` + - `*.gff`: Annotation in gff format + - `*.txt`: Annotation in text format + - `*.faa`: Protein sequences in fasta format See [Prokka's documentation](https://github.com/tseemann/prokka#output-files) for a full description of all output files. ![Prokka annotation](images/prokka.png) -- `DFAST/{sample_id}_results/` +- `DFAST/{ID}_results/` - `genome.gff`: Annotation in gff format - `statistics.txt`: Annotation statistics in text format - `protein.faa`: Protein sequences in fasta format @@ -233,6 +233,5 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ - `pipeline_info/` - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. - - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
    diff --git a/docs/usage.md b/docs/usage.md index e35d36dd..c9c898ca 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -36,14 +36,14 @@ shortNlong ./data/S1_R1.fastq.gz ./data/S1_R2.fastq.gz ./data/S1_long_f | `Fast5` | Full path to a folder containing Fast5 file(s) for ONT long reads. `NA` indicates that there are no Fast5 files available. | | `GenomeSize` | Expected genome size. For example, `2.8m` means 2.8 million basepairs genome size expected. This is only used by Canu assembler. `NA` indicates that this value is unknown. | -An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. +An [example samplesheet](../assets/samplesheet.tsv) has been provided with the pipeline. ## Running the pipeline The typical command for running the pipeline is as follows: ```console -nextflow run nf-core/bacass --input samplesheet.csv -profile docker --skip_kraken2 +nextflow run nf-core/bacass --input samplesheet.tsv -profile docker --skip_kraken2 ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -72,9 +72,8 @@ nextflow run nf-core/bacass -profile docker -params-file params.yaml with `params.yaml` containing: ```yaml -input: './samplesheet.csv' +input: './samplesheet.tsv' outdir: './results/' -genome: 'GRCh37' <...> ``` diff --git a/modules/local/pycoqc.nf b/modules/local/pycoqc.nf index 42030bf3..c3edb434 100644 --- a/modules/local/pycoqc.nf +++ b/modules/local/pycoqc.nf @@ -1,5 +1,4 @@ process PYCOQC { - tag "$fast5" label 'process_medium' conda "bioconda::pycoqc=2.5.2" @@ -23,7 +22,7 @@ process PYCOQC { def prefix = task.ext.prefix ?: "${meta.id}" def run_summary = file("${fast5}/sequencing_summary.txt").exists() ? "cp ${fast5}/sequencing_summary.txt ./sequencing_summary.txt" : "Fast5_to_seq_summary -f $fast5 -t ${task.cpus} -s './sequencing_summary.txt' --verbose_level 2" def barcode_me = file("${fast5}/barcoding_sequencing.txt").exists() ? "-b ${fast5}/barcoding_sequencing.txt" : '' - + """ $run_summary @@ -39,4 +38,4 @@ process PYCOQC { pycoqc: \$(pycoQC --version 2>&1 | sed 's/^.*pycoQC v//; s/ .*\$//') END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index f2b65abc..00000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -1,31 +0,0 @@ -process SAMPLESHEET_CHECK { - tag "$samplesheet" - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - path samplesheet - - output: - path '*.csv' , emit: csv - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in nf-core/bacass/bin/ - """ - check_samplesheet.py \\ - $samplesheet \\ - samplesheet.valid.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/nextflow.config b/nextflow.config index cc5c6a33..10e4431a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -10,81 +10,79 @@ params { // Input options - input = null + input = null // QC and trimming options - save_trimmed_fail = false - save_merged = false + save_trimmed_fail = false + save_merged = false // Contamination_screening - kraken2db = "" + kraken2db = "" // Assembly parameters - assembler = 'unicycler' //allowed are unicycler, canu, miniasm - assembly_type = 'short' //allowed are short, long, hybrid (hybrid works only with Unicycler) - unicycler_args = "" - canu_mode = '-nanopore' // allowed modes: ["-pacbio", "-nanopore", "-pacbio-hifi"] - canu_args = '' //Default no extra options, can be adjusted by the user + assembler = 'unicycler' //allowed are unicycler, canu, miniasm + assembly_type = 'short' //allowed are short, long, hybrid (hybrid works only with Unicycler) + unicycler_args = "" + canu_mode = '-nanopore' // allowed modes: ["-pacbio", "-nanopore", "-pacbio-hifi"] + canu_args = '' //Default no extra options, can be adjusted by the user // Assembly polishing - polish_method = 'medaka' + polish_method = 'medaka' // Annotation - annotation_tool = 'prokka' - prokka_args = "" - dfast_config = "$projectDir/assets/test_config_dfast.py" + annotation_tool = 'prokka' + prokka_args = "" + dfast_config = "$projectDir/assets/test_config_dfast.py" // Skipping options - skip_fastqc = false - skip_fastp = false - skip_kraken2 = false - skip_pycoqc = false - skip_annotation = false - skip_polish = false - skip_multiqc = false + skip_fastqc = false + skip_fastp = false + skip_kraken2 = false + skip_pycoqc = false + skip_annotation = false + skip_polish = false + skip_multiqc = false // MultiQC options - multiqc_config = null - multiqc_title = null - multiqc_logo = null - max_multiqc_email_size = '25.MB' - multiqc_methods_description = null + multiqc_config = null + multiqc_title = null + multiqc_logo = null + max_multiqc_email_size = '25.MB' + multiqc_methods_description = null // Boilerplate options - outdir = null - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - hook_url = null - help = false - validate_params = true - schema_ignore_params = 'modules,igenomes_base' - version = false + outdir = null + publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false + monochrome_logs = false + hook_url = null + help = false + validate_params = true + schema_ignore_params = 'modules,igenomes_base' + version = false // Config options - config_profile_name = null - config_profile_description = null - custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_contact = null - config_profile_url = null - + config_profile_name = null + config_profile_description = null + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + config_profile_contact = null + config_profile_url = null // Max resource options // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' + max_memory = '128.GB' + max_cpus = 16 + max_time = '240.h' // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes' - validationShowHiddenParams = false - validate_params = true - + validationFailUnrecognisedParams= false + validationLenientMode = false + validationSchemaIgnoreParams = 'genomes' + validationShowHiddenParams = false + validate_params = true } // Load base.config by default for all pipelines @@ -140,7 +138,7 @@ profiles { apptainer.enabled = false } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true @@ -226,7 +224,7 @@ env { } // Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +process.shell = ['/bin/bash', '-euo', 'pipefail'] def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { @@ -254,7 +252,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' version = '2.1.0dev' - doi = '' + doi = '10.5281/zenodo.2669428' } // Load modules.config for DSL2 module specific options diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 613ea0f6..14ad29c4 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -57,13 +57,12 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil // // MODULE: Local to the pipeline // -include { NANOPLOT_CUSTOM } from '../modules/local/nanoplot_custom' include { PYCOQC } from '../modules/local/pycoqc' include { UNICYCLER } from '../modules/local/unicycler' include { NANOPOLISH } from '../modules/local/nanopolish' include { MEDAKA } from '../modules/local/medaka' include { KRAKEN2_DB_PREPARATION } from '../modules/local/kraken2_db_preparation' -include { DFAST } from '../modules/local/dfast' +include { DFAST } from '../modules/local/dfast' // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules @@ -78,7 +77,8 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check' // // MODULE: Installed directly from nf-core/modules -// +// +include { NANOPLOT } from '../modules/nf-core/nanoplot/main' include { PORECHOP_PORECHOP } from '../modules/nf-core/porechop/porechop/main' include { CANU } from '../modules/nf-core/canu/main' include { MINIMAP2_ALIGN } from '../modules/nf-core/minimap2/align/main' @@ -122,7 +122,7 @@ workflow BACASS { ) // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ - // ! There is currently no tooling to help you write a sample sheet schema + // ! There is currently no tooling to help you write a sample sheet schema // // SUBWORKFLOW: Short reads QC and trim adapters @@ -140,10 +140,10 @@ workflow BACASS { // // MODULE: Nanoplot, quality check for nanopore reads and Quality/Length Plots // - NANOPLOT_CUSTOM ( + NANOPLOT ( INPUT_CHECK.out.longreads ) - ch_versions = ch_versions.mix(NANOPLOT_CUSTOM.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(NANOPLOT.out.versions.first().ifEmpty(null)) // // MODULE: PYCOQC, quality check for nanopore reads and Quality/Length Plots @@ -253,7 +253,7 @@ workflow BACASS { MINIASM.out.assembly.map { meta, assembly -> assembly }, false, false, - false + false ) ch_versions = ch_versions.mix(MINIMAP2_CONSENSUS.out.versions.first().ifEmpty(null)) @@ -277,13 +277,13 @@ workflow BACASS { ch_for_assembly .join( ch_assembly ) .set { ch_for_polish } - + MINIMAP2_POLISH ( ch_for_polish.map { meta, sr, lr, fasta -> tuple(meta, lr) }, ch_for_polish.map { meta, sr, lr, fasta -> fasta }, true, false, - false + false ) ch_versions = ch_versions.mix(MINIMAP2_POLISH.out.versions.first().ifEmpty(null)) @@ -313,11 +313,11 @@ workflow BACASS { .join( ch_assembly ) .map { meta, sr, lr, assembly -> tuple(meta, lr, assembly) } .set { ch_for_medaka } - + MEDAKA ( ch_for_medaka.dump(tag: 'into_medaka') ) ch_versions = ch_versions.mix(MEDAKA.out.versions.first().ifEmpty(null)) } - + // // MODULE: Kraken2, QC for sample purity // From 3abc9ed4f2f3dd1ee05b81fda2cc0146f9bf20e9 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 19 Sep 2023 17:14:07 +0200 Subject: [PATCH 20/21] fix prettier after adding code-reviewer suggestions --- CHANGELOG.md | 45 ++++++++++++++++++++++----------------------- 1 file changed, 22 insertions(+), 23 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e70f466..734a2e91 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,35 +28,34 @@ This version merges the nf-core template update v2.9. It also updates modules or - [#61](https://github.com/nf-core/bacass/issues/61) - Update local/modules to nf-core/modules plus version update. -| Tool | Previous version | New version | -| ------ | ---------------- | ----------- | -| Canu | 2.1.1 | 2.2 | -| Minimap2 | 2.21 | 2.2 | -| Miniasm | 0.3 | - | -| Racon | 1.4.20-1 | - | +| Tool | Previous version | New version | +| -------- | ---------------- | ----------- | +| Canu | 2.1.1 | 2.2 | +| Minimap2 | 2.21 | 2.2 | +| Miniasm | 0.3 | - | +| Racon | 1.4.20-1 | - | - Update already nf-core modules -| Tool | Previous version | New version | -| ------ | ---------------- | ----------- | -| Fastqc | 0.11.9 | - | -| Samtools | 1.13 | 2.1.2 | -| Kraken2 | 2.1.1 | 2.1.2 | -| Quast | 5.0.2 | 5.2.0 | -| Prokka | 1.14.6 | - | -| Multiqc | 1.10.1 | 1.15 | +| Tool | Previous version | New version | +| -------- | ---------------- | ----------- | +| Fastqc | 0.11.9 | - | +| Samtools | 1.13 | 2.1.2 | +| Kraken2 | 2.1.1 | 2.1.2 | +| Quast | 5.0.2 | 5.2.0 | +| Prokka | 1.14.6 | - | +| Multiqc | 1.10.1 | 1.15 | - Refactor `local/modules` making them follow nf-core v2.9 structure/fashion. -| Tool | Previous version | New version | -| ------ | ---------------- | ----------- | -| Dfast | 1.2.14 | - | -| Medaka | 1.4.3-0 | - | -| Nanoplot | 1.38.0 | 1.41.6 | - | Nanopolish | 0.13.2-5 | 0.14.0 | - | Pycoqc | 2.5.2 | - | - | Unicycler | 0.4.8 | - | - +| Tool | Previous version | New version | +| ---------- | ---------------- | ----------- | +| Dfast | 1.2.14 | - | +| Medaka | 1.4.3-0 | - | +| Nanoplot | 1.38.0 | 1.41.6 | +| Nanopolish | 0.13.2-5 | 0.14.0 | +| Pycoqc | 2.5.2 | - | +| Unicycler | 0.4.8 | - | ### `Deprecated` From 5c6fbeed4d25f72f812ea2c5c952636ead7b73c0 Mon Sep 17 00:00:00 2001 From: Dani VM Date: Tue, 19 Sep 2023 22:47:33 +0200 Subject: [PATCH 21/21] removed lines causing warnings --- workflows/bacass.nf | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 14ad29c4..5b6c5eb0 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -143,7 +143,7 @@ workflow BACASS { NANOPLOT ( INPUT_CHECK.out.longreads ) - ch_versions = ch_versions.mix(NANOPLOT.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(NANOPLOT.out.versions.ifEmpty(null)) // // MODULE: PYCOQC, quality check for nanopore reads and Quality/Length Plots @@ -153,7 +153,7 @@ workflow BACASS { PYCOQC ( INPUT_CHECK.out.fast5.dump(tag: 'fast5') ) - versions = ch_versions.mix(PYCOQC.out.versions.first().ifEmpty(null)) + versions = ch_versions.mix(PYCOQC.out.versions.ifEmpty(null)) } // @@ -163,7 +163,7 @@ workflow BACASS { PORECHOP_PORECHOP ( INPUT_CHECK.out.longreads.dump(tag: 'longreads') ) - ch_versions = ch_versions.mix( PORECHOP_PORECHOP.out.versions.first().ifEmpty(null) ) + ch_versions = ch_versions.mix( PORECHOP_PORECHOP.out.versions.ifEmpty(null) ) } // @@ -223,7 +223,7 @@ workflow BACASS { ch_for_assembly.map { meta, reads, lr -> meta.genome_size } ) ch_assembly = ch_assembly.mix( CANU.out.assembly.dump(tag: 'canu') ) - ch_versions = ch_versions.mix(CANU.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(CANU.out.versions.ifEmpty(null)) } // @@ -236,7 +236,7 @@ workflow BACASS { false, false ) - ch_versions = ch_versions.mix(MINIMAP2_ALIGN.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(MINIMAP2_ALIGN.out.versions.ifEmpty(null)) ch_for_assembly .join(MINIMAP2_ALIGN.out.paf) @@ -246,7 +246,7 @@ workflow BACASS { MINIASM ( ch_for_miniasm ) - ch_versions = ch_versions.mix(MINIASM.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(MINIASM.out.versions.ifEmpty(null)) MINIMAP2_CONSENSUS ( ch_for_assembly.map{ meta,sr,lr -> tuple(meta,lr) }, @@ -255,7 +255,7 @@ workflow BACASS { false, false ) - ch_versions = ch_versions.mix(MINIMAP2_CONSENSUS.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(MINIMAP2_CONSENSUS.out.versions.ifEmpty(null)) ch_for_assembly .join(MINIASM.out.assembly) @@ -267,7 +267,7 @@ workflow BACASS { ch_for_racon ) ch_assembly = ch_assembly.mix( RACON.out.improved_assembly.dump(tag: 'miniasm') ) - ch_versions = ch_versions.mix(RACON.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(RACON.out.versions.ifEmpty(null)) } // @@ -285,12 +285,12 @@ workflow BACASS { false, false ) - ch_versions = ch_versions.mix(MINIMAP2_POLISH.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(MINIMAP2_POLISH.out.versions.ifEmpty(null)) SAMTOOLS_INDEX ( MINIMAP2_POLISH.out.bam.dump(tag: 'samtools_sort') ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.ifEmpty(null)) ch_for_polish // tuple val(meta), val(reads), file(longreads), file(assembly) .join( MINIMAP2_POLISH.out.bam ) // tuple val(meta), file(bam) @@ -302,7 +302,7 @@ workflow BACASS { NANOPOLISH ( ch_for_nanopolish.dump(tag: 'into_nanopolish') ) - ch_versions = ch_versions.mix(NANOPOLISH.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(NANOPOLISH.out.versions.ifEmpty(null)) } // @@ -315,7 +315,7 @@ workflow BACASS { .set { ch_for_medaka } MEDAKA ( ch_for_medaka.dump(tag: 'into_medaka') ) - ch_versions = ch_versions.mix(MEDAKA.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(MEDAKA.out.versions.ifEmpty(null)) } // @@ -331,7 +331,7 @@ workflow BACASS { false, false ) - ch_versions = ch_versions.mix(KRAKEN2.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(KRAKEN2.out.versions.ifEmpty(null)) KRAKEN2_LONG ( ch_for_kraken2_long .map { meta, reads -> @@ -345,7 +345,7 @@ workflow BACASS { false, false ) - ch_versions = ch_versions.mix(KRAKEN2_LONG.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(KRAKEN2_LONG.out.versions.ifEmpty(null)) } // @@ -361,7 +361,7 @@ workflow BACASS { [[:],[]], [[:],[]] ) - ch_versions = ch_versions.mix(QUAST.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(QUAST.out.versions.ifEmpty(null)) // // MODULE: PROKKA, gene annotation @@ -369,14 +369,14 @@ workflow BACASS { if ( !params.skip_annotation && params.annotation_tool == 'prokka' ) { GUNZIP ( ch_assembly ) ch_to_prokka = GUNZIP.out.gunzip - ch_versions = ch_versions.mix(GUNZIP.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(GUNZIP.out.versions.ifEmpty(null)) PROKKA ( ch_to_prokka, [], [] ) - ch_versions = ch_versions.mix(PROKKA.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(PROKKA.out.versions.ifEmpty(null)) } // @@ -388,7 +388,7 @@ workflow BACASS { ch_assembly, Channel.value(params.dfast_config ? file(params.dfast_config) : "") ) - ch_versions = ch_versions.mix(DFAST.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(DFAST.out.versions.ifEmpty(null)) } //