Template update

.devcontainer/devcontainer.json

@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

.github/CONTRIBUTING.md

@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-> If you need help using or modifying nf-core/crisprseq then the best place to ask is on the nf-core Slack [#crisprseq](https://nfcore.slack.com/channels/crisprseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/crisprseq then the best place to ask is on the nf-core Slack [#crisprseq](https://nfcore.slack.com/channels/crisprseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 ## Contribution workflow
 

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies

.github/workflows/release-announcments.yml

@@ -0,0 +1,68 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: rzr/fediverse-action@master
+        with:
+          access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+          host: "mstdn.science" # custom host if not "mastodon.social" (default)
+          # GitHub event payload
+          # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+          message: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+
+  send-tweet:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: pip install tweepy==4.14.0
+      - name: Send tweet
+        shell: python
+        run: |
+          import os
+          import tweepy
+
+          client = tweepy.Client(
+              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
+              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
+              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
+              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
+          )
+          tweet = os.getenv("TWEET")
+          client.create_tweet(text=tweet)
+        env:
+          TWEET: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
+          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
+          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
+          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
+
+  bsky-post:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: zentered/[email protected]
+        with:
+          post: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+        env:
+          BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
+          BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
+          #

CITATIONS.md

@@ -16,7 +16,7 @@
 
 - [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/.
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 

README.md

@@ -1,6 +1,7 @@
 # ![nf-core/crisprseq](docs/images/nf-core-crisprseq_logo_light.png#gh-light-mode-only) ![nf-core/crisprseq](docs/images/nf-core-crisprseq_logo_dark.png#gh-dark-mode-only)
 
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/crisprseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.8116072-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.8116072)
+[![GitHub Actions CI Status](https://github.com/nf-core/crisprseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/crisprseq/actions?query=workflow%3A%22nf-core+CI%22)
+[![GitHub Actions Linting Status](https://github.com/nf-core/crisprseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/crisprseq/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/crisprseq/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%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/)
@@ -63,10 +64,14 @@ For crispr screening:
 
 ## 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_targeted` or `-profile test_screening` before running the workflow on actual data.
+:::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.
+:::
+
+<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
+     Explain what rows and columns represent. For instance (please edit as appropriate):
 
 First, prepare a samplesheet with your input data that looks as follows:
 
@@ -94,10 +99,11 @@ Now, you can run the pipeline using:
 nextflow run nf-core/crisprseq --input samplesheet.csv --analysis <targeted/screening> --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
 ```
 
-> **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).
+:::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).
+:::
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/crisprseq/usage) and the [parameter documentation](https://nf-co.re/crisprseq/parameters).
 
@@ -109,10 +115,7 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/crisprseq targeted is based on [CRISPR-A](https://doi.org/10.1101/2022.09.02.506351) [[Sanvicente-García, et.al. (2023)](https://doi.org/10.1371/journal.pcbi.1011137)], originally written by Marta Sanvicente García at [Translational Synthetic Biology](https://synbio.upf.edu/) from [Universitat Pompeu Fabra](https://www.upf.edu/home).
-It was re-written in Nextflow DSL2 and is primarily maintained by Júlia Mir Pedrol (@mirpedrol) at [Quantitative Biology Center (QBiC)](https://www.qbic.uni-tuebingen.de/) from [Universität Tübingen](https://uni-tuebingen.de/en/).
-
-nf-core/crisprseq screening was written and is primarly maintained by Laurence Kuhlburger (@LaurenceKuhl) at [Quantitative Biology Center (QBiC)](https://www.qbic.uni-tuebingen.de/) from [Universität Tübingen](https://uni-tuebingen.de/en/).
+nf-core/crisprseq was originally written by Júlia Mir Pedrol, Laurence Kuhlburger.
 
 <!--We thank the following people for their extensive assistance in the development of this pipeline:
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/crisprseq" target="_blank">nf-core/crisprseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/crisprseq/releases/tag/dev" target="_blank">nf-core/crisprseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/crisprseq/2.0.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/crisprseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-crisprseq-methods-description":
     order: -1000

conf/modules.config

@@ -286,4 +286,13 @@ process {
         ]
     }
 
+    withName: 'MULTIQC' {
+        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+        publishDir = [
+            path: { "${params.outdir}/multiqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
 }

docs/output.md

@@ -2,9 +2,70 @@
 
 ## Introduction
 
-This document describes the output produced by the pipeline.
+This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
 
-Please refer to the respective Output documentation:
+The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
-- [Output targeted](output/targeted.md)
-- [Output screening](output/screening.md)
+<!-- TODO nf-core: Write this documentation describing your workflow's output -->
+
+## Pipeline overview
+
+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
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `fastqc/`
+  - `*_fastqc.html`: FastQC report containing quality metrics.
+  - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
+
+</details>
+
+[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
+
+![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
+
+![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
+
+![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
+
+:::note
+The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+:::
+
+### MultiQC
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `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.
+
+</details>
+
+[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
+
+Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+
+### Pipeline information
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `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`.
+  - Parameters used by the pipeline run: `params.json`.
+
+</details>
+
+[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.

docs/usage.md

@@ -40,7 +40,9 @@ 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 <file>`.
 
-> ⚠️ Do not use `-c <file>` 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).
+:::warning
+Do not use `-c <file>` 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:
 
@@ -77,11 +79,13 @@ This version number will be logged in reports when you run the pipeline, so that
 
 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.
+:::tip
+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
 
-:::info
+:::note
 These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
 :::
 
@@ -91,7 +95,7 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 
 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.
 
-:::note
+:::info
 We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 :::
 

lib/NfcoreTemplate.groovy

@@ -3,6 +3,7 @@
 //
 
 import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
 
 class NfcoreTemplate {
 
@@ -222,6 +223,21 @@ class NfcoreTemplate {
         }
     }
 
+    //
+    // Dump pipeline parameters in a json file
+    //
+    public static void dump_parameters(workflow, params) {
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+
+        def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+        def output_pf  = new File(output_d, "params_${timestamp}.json")
+        def jsonStr    = JsonOutput.toJson(params)
+        output_pf.text = JsonOutput.prettyPrint(jsonStr)
+    }
+
     //
     // Print pipeline summary on completion
     //

lib/WorkflowCrisprseq.groovy

@@ -75,7 +75,7 @@ class WorkflowCrisprseq {
 
     public static String toolCitationText(params) {
 
-        // TODO Optionally add in-text citation tools to this list.
+        // TODO nf-core: 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 = [