Merge pull request #143 from nf-core/dev

Dev > Master for 1.2 release

.github/CONTRIBUTING.md

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

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,31 +1,42 @@
+# nf-core/chipseq 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/chipseq:1.0.0] -->
 
-#### Container engine:
- - Engine: [e.g. Conda, Docker or Singularity]
- - version: [e.g. 1.0.0]
- - Image tag: [e.g. nfcore/chipseq: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/chipseq 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/chipseq!
+# nf-core/chipseq 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/chipseq!
+
+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/chipseq branch on the nf-core/test-datasets repo]( https://github.com/nf-core/test-datasets/pull/new/nf-core/chipseq)
- - [ ] 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/chipseq/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/chipseq branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/chipseq)
+- [ ] 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/chipseq/tree/master/.github/CONTRIBUTING.md)

.github/markdownlint.yml

@@ -3,3 +3,7 @@ default: true,
 line-length: false
 no-duplicate-header:
     siblings_only: true
+MD033:
+    allowed_elements: [details, summary, p, img]
+MD007:
+    indent: 4

.github/workflows/awsfulltest.yml

@@ -0,0 +1,36 @@
+name: nf-core AWS full size tests
+# This workflow is triggered on releases.
+# It runs the -profile 'test_full' on AWS batch
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  run-awstest:
+    if: github.repository == 'nf-core/chipseq'
+    name: Run AWS test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Miniconda
+        uses: goanpeca/setup-miniconda@v1.0.2
+        with:
+          auto-update-conda: true
+          python-version: 3.7
+      - name: Install awscli
+        run: conda install -c conda-forge awscli
+      - name: Start AWS batch job
+        env:
+          AWS_ACCESS_KEY_ID: ${{secrets.AWS_ACCESS_KEY_ID}}
+          AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_SECRET_ACCESS_KEY}}
+          TOWER_ACCESS_TOKEN: ${{secrets.AWS_TOWER_TOKEN}}
+          #AWS_JOB_DEFINITION: ${{secrets.AWS_JOB_DEFINITION}}
+          AWS_JOB_QUEUE: ${{secrets.AWS_JOB_QUEUE}}
+          AWS_S3_BUCKET: ${{secrets.AWS_S3_BUCKET}}
+        run: | # Submits job to AWS batch using a 'nextflow-4GiB' job definition. Setting JVM options to "-XX:+UseG1GC" for more efficient garbage collection when staging remote files.
+          aws batch submit-job \
+          --region eu-west-1 \
+          --job-name nf-core-chipseq \
+          --job-queue $AWS_JOB_QUEUE \
+          --job-definition nextflow-4GiB \
+          --container-overrides '{"command": ["nf-core/chipseq", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/chipseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/chipseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}, {"name": "NXF_OPTS", "value": "-XX:+UseG1GC"}]}'

.github/workflows/awstest.yml

@@ -0,0 +1,38 @@
+name: nf-core AWS test
+# This workflow is triggered on push to the master branch.
+# It runs the -profile 'test' on AWS batch
+
+on:
+  push:
+    branches:
+        - master
+        - dev # just for testing purposes, to be removed
+
+jobs:
+  run-awstest:
+    if: github.repository == 'nf-core/chipseq'
+    name: Run AWS test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Miniconda
+        uses: goanpeca/setup-miniconda@v1.0.2
+        with:
+          auto-update-conda: true
+          python-version: 3.7
+      - name: Install awscli
+        run: conda install -c conda-forge awscli
+      - name: Start AWS batch job
+        env:
+          AWS_ACCESS_KEY_ID: ${{secrets.AWS_ACCESS_KEY_ID}}
+          AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_SECRET_ACCESS_KEY}}
+          TOWER_ACCESS_TOKEN: ${{secrets.AWS_TOWER_TOKEN}}
+          #AWS_JOB_DEFINITION: ${{secrets.AWS_JOB_DEFINITION}}
+          AWS_JOB_QUEUE: ${{secrets.AWS_JOB_QUEUE}}
+          AWS_S3_BUCKET: ${{secrets.AWS_S3_BUCKET}}
+        run: | # Submits job to AWS batch using a 'nextflow-4GiB' job definition. Setting JVM options to "-XX:+UseG1GC" for more efficient garbage collection when staging remote files.
+          aws batch submit-job \
+          --region eu-west-1 \
+          --job-name nf-core-chipseq \
+          --job-queue $AWS_JOB_QUEUE \
+          --job-definition nextflow-4GiB \
+          --container-overrides '{"command": ["nf-core/chipseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/chipseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/chipseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}, {"name": "NXF_OPTS", "value": "-XX:+UseG1GC"}]}'

.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/chipseq ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]