Merge pull request #71 from MaxUlysse/DOCS

Improve tests and docs

Author: maxulysse

.github/CONTRIBUTING.md

@@ -1,47 +1,57 @@
 # nf-core/sarek: Contributing Guidelines
 
-Hi there! Many thanks for taking an interest in improving nf-core/sarek.
+Hi there!
+Many thanks for taking an interest in improving nf-core/sarek.
 
-We try to manage the required tasks for nf-core/sarek 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/sarek 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/sarek 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/sarek then the best place to ask is on the nf-core Slack [#sarek](https://nfcore.slack.com/channels/sarek) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
-If you'd like to write some code for nf-core/sarek, the standard workflow
-is as follows:
 
-1. Check that there isn't already an issue about your idea in the
-   [nf-core/sarek issues](https://github.com/nf-core/sarek/issues) to avoid
-   duplicating work.
+If you'd like to write some code for nf-core/sarek, the standard workflow is as follows:
+
+1. Check that there isn't already an issue about your idea in the [nf-core/sarek issues](https://github.com/nf-core/sarek/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/sarek repository](https://github.com/nf-core/sarek) to your GitHub account
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/sarek repository](https://github.com/nf-core/sarek) 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/sarek documentation](https://github.com/nf-core/sarek#documentation) and don't hesitate to get in touch on the [sarek pipeline channel](https://nfcore.slack.com/channels/sarek) on [Slack](https://nf-co.re/join/slack).
+
+For further information/help, please consult the [nf-core/sarek documentation](https://nf-co.re/sarek/docs) and don't hesitate to get in touch on the nf-core Slack [#sarek](https://nfcore.slack.com/channels/sarek) channel ([join our Slack here](https://nf-co.re/join/slack)).

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,31 +1,42 @@
+# nf-core/sarek 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/sarek:2.5.1] -->
 
-#### Container engine:
- - Engine: [e.g. Conda, Docker or Singularity]
- - version: [e.g. 1.0.0]
- - Image tag: [e.g. nfcore/sarek:1.0.0]
+## Additional context
 
-#### Additional context
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,16 +1,24 @@
+# nf-core/sarek 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

@@ -1,16 +1,19 @@
-Many thanks to contributing to nf-core/sarek!
+# nf-core/sarek pull request
+
+Many thanks for contributing to nf-core/sarek!
 
 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/sarek branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/sarek)
- - [ ] 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:** [guidelines](https://github.com/nf-core/sarek/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/sarek branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/sarek)
+- [ ] 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/sarek/tree/master/.github/CONTRIBUTING.md)

.github/workflows/branch.yml

@@ -7,10 +7,10 @@ on:
 
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     steps:
       # PRs are only ok if coming from an nf-core dev branch
       - uses: actions/checkout@v1
       - name: Check PRs
         run: |
-          { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == patch* ]]
+          { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]

.github/workflows/ci-extra.yml

@@ -3,22 +3,64 @@ name: sarek extra CI
 on: [push, pull_request]  
 
 jobs:
-  test:
-    runs-on: ubuntu-latest
+  profile:
+    runs-on: ubuntu-18.04
     strategy:
       matrix:
-        test: [ANNOTATESNPEFF, GERMLINE, SOMATIC, SPLITFASTQ, TARGETED]
-        nxf_ver: ['19.04.0', '']
+        profile: [test_splitfastq, test_targeted]
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow
         run: |
-          export NXF_VER=${{ matrix.nxf_ver }}
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
+        env:
+          NXF_VER: '19.04.0'
       - name: Download image
         run: |
-          ${GITHUB_WORKSPACE}/scripts/download_image.sh -n docker --source-version dev --target-version dev --test ${{ matrix.test }}
+          docker pull nfcore/sarek:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run test
         run: |
-          ${GITHUB_WORKSPACE}/scripts/run_tests.sh --test ${{ matrix.test }} --verbose
+          nextflow run . -profile ${{ matrix.profile }},docker --verbose
+  tools:
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        tool: [Haplotypecaller, Freebayes, Manta, mpileup, Mutect2, Strelka]
+    steps:
+      - uses: actions/checkout@v1
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+        env:
+          NXF_VER: '19.04.0'
+      - name: Download image
+        run: |
+          docker pull nfcore/sarek:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
+      - name: Run test
+        run: |
+          nextflow run . -profile test_tool,docker --verbose --tools ${{ matrix.tool }}
+  annotation:
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        annotator: [snpeff]
+        specie: [GRCh37]
+    steps:
+      - uses: actions/checkout@v1
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+        env:
+          NXF_VER: '19.04.0'
+      - name: Download image
+        run: |
+          docker pull nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }}
+          docker tag nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }} nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }}
+      - name: Run test
+        run: |
+          nextflow run . -profile test_annotation,docker --verbose --tools ${{ matrix.annotator }}

.github/workflows/ci.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     strategy:
       matrix:
         nxf_ver: ['19.04.0', '']

.github/workflows/linting.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 jobs:
   Markdown:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     steps:
       - uses: actions/checkout@v1
       - uses: actions/setup-node@v1
@@ -17,7 +17,7 @@ jobs:
         run: |
           markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
   YAML:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     steps:
       - uses: actions/checkout@v1
       - uses: actions/setup-node@v1
@@ -30,7 +30,7 @@ jobs:
         run: |
           yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml")
   nf-core:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow