Merge pull request #18 from nf-core/dev

Dev > Master

.github/CONTRIBUTING.md

@@ -1,47 +1,57 @@
 # nf-core/imcyto: Contributing Guidelines
 
-Hi there! Many thanks for taking an interest in improving nf-core/imcyto.
+Hi there!
+Many thanks for taking an interest in improving nf-core/imcyto.
 
-We try to manage the required tasks for nf-core/imcyto using GitHub issues, you probably came to this page when creating one. 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/imcyto then the best place to ask is on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
+We try to manage the required tasks for nf-core/imcyto using GitHub issues, you probably came to this page when creating one.
+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/imcyto then the best place to ask is on the nf-core Slack [#imcyto](https://nfcore.slack.com/channels/imcyto) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
-If you'd like to write some code for nf-core/imcyto, the standard workflow
-is as follows:
 
-1. Check that there isn't already an issue about your idea in the
-   [nf-core/imcyto issues](https://github.com/nf-core/imcyto/issues) to avoid
-   duplicating work.
+If you'd like to write some code for nf-core/imcyto, the standard workflow is as follows:
+
+1. Check that there isn't already an issue about your idea in the [nf-core/imcyto issues](https://github.com/nf-core/imcyto/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 the [nf-core/imcyto repository](https://github.com/nf-core/imcyto) to your GitHub account
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/imcyto repository](https://github.com/nf-core/imcyto) to your GitHub account
 3. Make the necessary changes / additions within your forked repository
-4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged.
-
-If you're not used to this workflow with git, you can start with some [basic docs from GitHub](https://help.github.com/articles/fork-a-repo/) or even their [excellent interactive tutorial](https://try.github.io/).
+4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
+If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
 
 ## Tests
-When you create a pull request with changes, [Travis CI](https://travis-ci.org/) will run automatic tests.
+
+When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 
 There are typically two types of tests that run:
 
 ### Lint Tests
-The nf-core has a [set of guidelines](http://nf-co.re/guidelines) which all pipelines must adhere to.
+
+`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
 To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
 ### Pipeline Tests
-Each nf-core pipeline should be set up with a minimal set of test-data.
-Travis CI then runs the pipeline on this data to ensure that it exists successfully.
+
+Each `nf-core` pipeline should be set up with a minimal set of test-data.
+`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
 If there are any failures then the automated tests fail.
-These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code.
+These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
+
+## Patch
+
+: 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.
 
 ## Getting help
-For further information/help, please consult the [nf-core/imcyto documentation](https://github.com/nf-core/imcyto#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
+
+For further information/help, please consult the [nf-core/imcyto documentation](https://nf-co.re/nf-core/imcyto/docs) and don't hesitate to get in touch on the nf-core Slack [#imcyto](https://nfcore.slack.com/channels/imcyto) channel ([join our Slack here](https://nf-co.re/join/slack)).

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,16 +1,24 @@
+# nf-core/imcyto feature request
+
 Hi there!
 
-Thanks for suggesting a new feature for the pipeline! Please delete this text and anything that's not relevant from the template below:
+Thanks for suggesting a new feature for the pipeline!
+Please delete this text and anything that's not relevant from the template below:
+
+## Is your feature request related to a problem? Please describe
 
-#### Is your feature request related to a problem? Please describe.
 A clear and concise description of what the problem is.
+
 Ex. I'm always frustrated when [...]
 
-#### Describe the solution you'd like
+## Describe the solution you'd like
+
 A clear and concise description of what you want to happen.
 
-#### Describe alternatives you've considered
+## Describe alternatives you've considered
+
 A clear and concise description of any alternative solutions or features you've considered.
 
-#### Additional context
+## Additional context
+
 Add any other context about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,15 +1,19 @@
-Many thanks to contributing to nf-core/imcyto!
+# nf-core/imcyto pull request
 
-Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
+Many thanks for contributing to nf-core/imcyto!
+
+Please fill in the appropriate checklist below (delete whatever is not relevant).
+These are the most common things requested on pull requests (PRs).
 
 ## PR checklist
- - [ ] 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 necessary, also make a PR on the [nf-core/imcyto branch on the nf-core/test-datasets repo]( https://github.com/nf-core/test-datasets/pull/new/nf-core/imcyto)
- - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
- - [ ] Make sure your code lints (`nf-core lint .`).
- - [ ] Documentation in `docs` is updated
- - [ ] `CHANGELOG.md` is updated
- - [ ] `README.md` is updated
-
-**Learn more about contributing:** https://github.com/nf-core/imcyto/tree/master/.github/CONTRIBUTING.md
+
+- [ ] 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 necessary, also make a PR on the [nf-core/imcyto branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/imcyto)
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] Make sure your code lints (`nf-core lint .`).
+- [ ] Documentation in `docs` is updated
+- [ ] `CHANGELOG.md` is updated
+- [ ] `README.md` is updated
+
+**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/imcyto/tree/master/.github/CONTRIBUTING.md)

.github/markdownlint.yml

@@ -1,9 +1,5 @@
 # Markdownlint configuration file
 default: true,
 line-length: false
-no-multiple-blanks: 0
-blanks-around-headers: false
-blanks-around-lists: false
-header-increment: false
 no-duplicate-header:
     siblings_only: true

.github/workflows/branch.yml

@@ -0,0 +1,16 @@
+name: nf-core branch protection
+# This workflow is triggered on PRs to master branch on the repository
+# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+on:
+  pull_request:
+    branches:
+    - master
+
+jobs:
+  test:
+    runs-on: ubuntu-18.04
+    steps:
+      # PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
+      - name: Check PRs
+        run: |
+          { [[ $(git remote get-url origin) == *nf-core/imcyto ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]

.github/workflows/ci.yml

@@ -0,0 +1,32 @@
+name: nf-core CI
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and current latest
+        nxf_ver: ['19.10.0', '']
+    steps:
+      - uses: actions/checkout@v1
+      - 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)
+      #  run: |
+      #    docker pull nfcore/imcyto:dev && docker tag nfcore/imcyto:dev nfcore/imcyto:dev
+      - name: Run the pipeline with .mcd input
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+      - name: Run the pipeline with .txt input
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_txt,docker
+      - name: Run the pipeline with .tiff input
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tiff,docker

.github/workflows/linting.yml

@@ -0,0 +1,41 @@
+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]  
+
+jobs:
+  Markdown:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v1
+      - uses: actions/setup-node@v1
+        with:
+          node-version: '10'
+      - name: Install markdownlint
+        run: |
+          npm install -g markdownlint-cli
+      - name: Run Markdownlint
+        run: |
+          markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+  nf-core:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - uses: actions/setup-python@v1
+        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
+        run: |
+          pip install nf-core
+      - name: Run nf-core lint
+        run: |
+          nf-core lint ${GITHUB_WORKSPACE}

.gitignore

@@ -3,5 +3,4 @@ work/
 data/
 results/
 .DS_Store
-tests/test_data
 *.pyc

.travis.yml

@@ -9,7 +9,13 @@ matrix:
 
 before_install:
   # PRs to master are only ok if coming from dev branch
-  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
+  #- '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ]) || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]'
+  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && ([ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ] || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]))'
+  # Pull the docker image first so the test doesn't wait for this
+  #- docker pull nfcore/imcyto:dev
+  # Fake the tag locally so that the pipeline runs properly
+  # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
+  #- docker tag nfcore/imcyto:dev nfcore/imcyto:dev
 
 install:
   # Install Nextflow
@@ -25,13 +31,17 @@ install:
   - sudo apt-get install npm && npm install -g markdownlint-cli
 
 env:
-  - NXF_VER='0.32.0' # Specify a minimum NF version that should be tested and work
+  - NXF_VER='19.10.0' # Specify a minimum NF version that should be tested and work
   - NXF_VER='' # Plus: get the latest NF version and check that it works
 
 script:
   # Lint the pipeline code
   - nf-core lint ${TRAVIS_BUILD_DIR}
   # Lint the documentation
   - markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
-  # Run the pipeline with the test profile
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker
+  # Run the pipeline with .mcd input
+  - nextflow run ${TRAVIS_BUILD_DIR} -ansi-log false -profile test,docker
+  # Run the pipeline with .txt input
+  - nextflow run ${TRAVIS_BUILD_DIR} -ansi-log false -profile test_txt,docker
+  # Run the pipeline with .tiff input
+  - nextflow run ${TRAVIS_BUILD_DIR} -ansi-log false -profile test_tiff,docker

CHANGELOG.md

@@ -1,4 +1,5 @@
 # nf-core/imcyto: Changelog
 
 ## v1.0dev - [date]
+
 Initial release of nf-core/imcyto, created with the [nf-core](http://nf-co.re/) template.

CITATIONS.md

@@ -0,0 +1,31 @@
+# nf-core/imcyto: Citations
+
+## Pipeline tools
+
+* [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.
+
+* [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.
+
+* [ilastik](https://www.ncbi.nlm.nih.gov/pubmed/31570887/)
+  > Berg S, Kutra D, Kroeger T, Straehle CN, Kausler BX, Haubold C, Schiegg M, Ales J, Beier T, Rudy M, Eren K, Cervantes JI, Xu B, Beuttenmueller F, Wolny A, Zhang C, Koethe U, Hamprecht FA, Kreshuk A. ilastik: interactive machine learning for (bio)image analysis. Nat Methods. 2019 Sep 30. doi: 10.1038/s41592-019-0582-9. [Epub ahead of print] Review. PubMed PMID: 31570887.
+
+* [histoCAT](https://www.ncbi.nlm.nih.gov/pubmed/28783155/)
+  > Schapiro D, Jackson HW, Raghuraman S, Fischer JR, Zanotelli VRT, Schulz D, Giesen C, Catena R, Varga Z, Bodenmiller B. histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data. Nat Methods. 2017 Sep;14(9):873-876. doi: 10.1038/nmeth.4391. Epub 2017 Aug 7. PubMed PMID: 28783155; PubMed Central PMCID: PMC5617107.
+
+* [imctools](https://github.com/BodenmillerGroup/imctools)
+
+* [Zanotelli & Bodenmiller, Jan 2019](https://github.com/BodenmillerGroup/ImcSegmentationPipeline/blob/development/documentation/imcsegmentationpipeline_documentation.pdf)
+
+* [CellProfiler Bodenmiller custom plugins](https://github.com/BodenmillerGroup/ImcPluginsCP)
+
+## Software packaging/containerisation tools
+
+* [BioContainers](https://www.ncbi.nlm.nih.gov/pubmed/28379341/)
+  > da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, 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.
+
+* [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/)

CODE_OF_CONDUCT.md

@@ -34,7 +34,7 @@ This Code of Conduct applies both within project spaces and in public spaces whe
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-core-invite.herokuapp.com/). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-co.re/join/slack). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
 
 Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
 

Dockerfile

@@ -1,11 +1,17 @@
-FROM nfcore/base
+FROM nfcore/base:1.7
 LABEL authors="Harshil Patel" \
-      description="Docker image containing majority of requirements for nf-core/imcyto pipeline"
+      description="Docker image containing all software requirements for the nf-core/imcyto pipeline"
 
 ## THIS DOCKER FILE ISNT REQUIRED FOR PIPELINE
 ## ALL DOCKER CONTAINERS ARE CURRENTLY OBTAINED FROM EXTERNAL SOURCES
 ## WAITING FOR LINT TESTS TO BE UPDATED BEFORE DELETING IT
 
+# Install the conda environment
 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
+
+# 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