Merge pull request #29 from nf-core/dev

Dev > Master for first release

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,31 +1,42 @@
+# nf-core/imcyto bug report
+
 Hi there!
 
-Thanks for telling us about a problem with the pipeline. Please delete this text and anything that's not relevant from the template below:
+Thanks for telling us about a problem with the pipeline.
+Please delete this text and anything that's not relevant from the template below:
+
+## Describe the bug
 
-#### Describe the bug
 A clear and concise description of what the bug is.
 
-#### Steps to reproduce
+## Steps to reproduce
+
 Steps to reproduce the behaviour:
+
 1. Command line: `nextflow run ...`
 2. See error: _Please provide your error message_
 
-#### Expected behaviour
+## Expected behaviour
+
 A clear and concise description of what you expected to happen.
 
-#### System:
- - Hardware: [e.g. HPC, Desktop, Cloud...]
- - Executor: [e.g. slurm, local, awsbatch...]
- - OS: [e.g. CentOS Linux, macOS, Linux Mint...]
- - Version [e.g. 7, 10.13.6, 18.3...]
+## System
+
+- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
+- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
+- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
+- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
+
+## Nextflow Installation
+
+- Version: <!-- [e.g. 19.10.0] -->
+
+## Container engine
 
-#### Nextflow Installation:
- - Version: [e.g. 0.31.0]
+- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- version: <!-- [e.g. 1.0.0] -->
+- Image tag: <!-- [e.g. nfcore/imcyto:1.0.0] -->
 
-#### Container engine:
- - Engine: [e.g. Conda, Docker or Singularity]
- - version: [e.g. 1.0.0]
- - Image tag: [e.g. nfcore/imcyto:1.0.0]
+## Additional context
 
-#### Additional context
 Add any other context about the problem here.

.github/workflows/ci.yml

@@ -5,28 +5,46 @@ on: [push, pull_request]
 
 jobs:
   test:
-    runs-on: ubuntu-18.04
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
         nxf_ver: ['19.10.0', '']
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
       - name: Install Nextflow
         run: |
-          export NXF_VER=${{ matrix.nxf_ver }}
-          export NXF_ANSI_LOG=false
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
-      #- name: Pull image (Cant pull standard single image for this pipeline as we are using individual BioContainers)
+      #- name: Pull docker image (Cant pull standard single image for this pipeline as we are using individual containers)
       #  run: |
-      #    docker pull nfcore/imcyto:dev && docker tag nfcore/imcyto:dev nfcore/imcyto:dev
+      #    docker pull nfcore/imcyto:dev
+      #    docker tag nfcore/imcyto:dev nfcore/imcyto:1.0.0
       - name: Run the pipeline with .mcd input
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
-      - name: Run the pipeline with .txt input
+
+  config:
+    env:
+      NXF_VER: '19.10.0'
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        config: [test_txt, test_tiff, test_skip_ilastik]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_txt,docker
-      - name: Run the pipeline with .tiff input
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      #- name: Pull docker image (Cant pull standard single image for this pipeline as we are using individual containers)
+      #  run: |
+      #    docker pull nfcore/imcyto:dev
+      #    docker tag nfcore/imcyto:dev nfcore/imcyto:1.0.0
+      - name: Run pipeline with various test configs
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tiff,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.config }},docker

.github/workflows/linting.yml

@@ -1,26 +1,39 @@
 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
-on: [push, pull_request]  
+on:
+  push:
+  pull_request:
+  release:
+    types: [published]
 
 jobs:
   Markdown:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
       - uses: actions/setup-node@v1
         with:
           node-version: '10'
       - name: Install markdownlint
-        run: |
-          npm install -g markdownlint-cli
+        run: npm install -g markdownlint-cli
       - name: Run Markdownlint
-        run: |
-          markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
-  nf-core:
+        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+  YAML:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
+      - uses: actions/setup-node@v1
+        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")
+  nf-core:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
@@ -29,13 +42,9 @@ jobs:
         with:
           python-version: '3.6'
           architecture: 'x64'
-      - name: Install pip
-        run: |
-          sudo apt install python3-pip
-          pip install --upgrade pip
-      - name: Install nf-core tools
+      - name: Install dependencies
         run: |
+          python -m pip install --upgrade pip
           pip install nf-core
       - name: Run nf-core lint
-        run: |
-          nf-core lint ${GITHUB_WORKSPACE}
+        run: nf-core lint ${GITHUB_WORKSPACE}

.gitignore

@@ -3,4 +3,6 @@ work/
 data/
 results/
 .DS_Store
+tests/
+testing/
 *.pyc

CHANGELOG.md

@@ -1,5 +1,8 @@
 # nf-core/imcyto: Changelog
 
-## v1.0dev - [date]
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## [1.0.0] - 2020-05-29
 
 Initial release of nf-core/imcyto, created with the [nf-core](http://nf-co.re/) template.

CITATIONS.md

@@ -1,9 +1,14 @@
 # nf-core/imcyto: Citations
 
-## Pipeline tools
+## [nf-core](https://www.ncbi.nlm.nih.gov/pubmed/32055031/)
+
+> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031. ReadCube: [Full Access Link](https://rdcu.be/b1GjZ).
+
+## [Nextflow](https://www.ncbi.nlm.nih.gov/pubmed/28398311/)
 
-* [Nextflow](https://www.ncbi.nlm.nih.gov/pubmed/28398311/)
-  > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
+> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
+
+## Pipeline tools
 
 * [CellProfiler](https://www.ncbi.nlm.nih.gov/pubmed/29969450/)
   > McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE. CellProfiler 3.0: Next-generation image processing for biology. PLoS Biol. 2018 Jul 3;16(7):e2005970. doi: 10.1371/journal.pbio.2005970. eCollection 2018 Jul. PubMed PMID: 29969450; PubMed Central PMCID: PMC6029841.
@@ -28,4 +33,4 @@
 * [Singularity](https://www.ncbi.nlm.nih.gov/pubmed/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.
 
-* [Docker](https://www.docker.com/)
+* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.7
+FROM nfcore/base:1.9
 LABEL authors="Harshil Patel" \
       description="Docker image containing all software requirements for the nf-core/imcyto pipeline"
 
@@ -11,7 +11,7 @@ COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-imcyto-1.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-imcyto-1.0.0/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-imcyto-1.0dev > nf-core-imcyto-1.0dev.yml
+RUN conda env export --name nf-core-imcyto-1.0.0 > nf-core-imcyto-1.0.0.yml

README.md

@@ -1,20 +1,18 @@
-# ![nfcore/imcyto](docs/images/nf-core-imcyto_logo.png)
+# ![nf-core/imcyto](docs/images/nf-core-imcyto_logo.png)
 
-[![Build Status](https://travis-ci.com/nf-core/imcyto.svg?branch=master)](https://travis-ci.com/nf-core/imcyto)
 [![GitHub Actions CI Status](https://github.com/nf-core/imcyto/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/imcyto/actions)
 [![GitHub Actions Linting Status](https://github.com/nf-core/imcyto/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/imcyto/actions)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
+<!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3697959.svg)](https://doi.org/10.5281/zenodo.3697959)  -->
 
 ## Introduction
 
-**nfcore/imcyto** is a bioinformatics analysis pipeline used for image segmentation and extraction of single cell expression data. This pipeline was generated for Imaging Mass Cytometry data, however, it is flexible enough to be applicable to other types of imaging data (e.g. immunofluorescence/immunohistochemistry data).
+**nfcore/imcyto** is a bioinformatics analysis pipeline used for image segmentation and extraction of single cell expression data. This pipeline was generated for Imaging Mass Cytometry data, however, it is flexible enough to be applicable to other types of imaging data e.g. immunofluorescence/immunohistochemistry data.
 
 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 comes with docker containers making installation trivial and results highly reproducible.
 
 ## Pipeline summary
 
-<!-- TODO nf-core: I think the schematic should also be added here as it nicely illustrates what this pipeline is for. -->
-
 1. Split image acquisition output files (`mcd`, `ome.tiff` or `txt`) by ROI and convert to individual `tiff` files for channels with names matching those defined in user-provided `metadata.csv` file. Full and ilastik stacks will be generated separately for all channels being analysed in single cell expression analysis, and for channels being used to generate the cell mask, respectively ([imctools](https://github.com/BodenmillerGroup/imctools)).
 
 2. Apply pre-processing filters to full stack `tiff` files ([CellProfiler](https://cellprofiler.org/)).
@@ -37,12 +35,10 @@ iii. Download the pipeline and test it on a minimal dataset with a single comman
 nextflow run nf-core/imcyto -profile test,<docker/singularity/institute>
 ```
 
-> 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 institute` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
+> 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 <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
 
 iv. Start running your own analysis!
 
-<!-- TODO nf-core: Update the default command above used to run the pipeline -->
-
 ```bash
 nextflow run nf-core/imcyto \
     --input "./inputs/*.mcd" \
@@ -90,7 +86,13 @@ For further information or help, don't hesitate to get in touch on [Slack](https
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi. -->
 <!-- If you use  nf-core/imcyto for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-You can cite the `nf-core` pre-print as follows:  
-> Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).
+You can cite the `nf-core` publication as follows:
+
+> **The nf-core framework for community-curated bioinformatics pipelines.**
+>
+> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
+>
+> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).  
+> ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.