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Merge pull request #492 from nf-core/dev
Dev -> Master 3.0.0
2 parents d16f8f8 + b212815 commit 4415e90

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‎.github/CONTRIBUTING.md‎

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# nf-core/methylseq: Contributing Guidelines
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# `nf-core/methylseq`: Contributing Guidelines
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Hi there!
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Many thanks for taking an interest in improving nf-core/methylseq.
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:warning: Only in the unlikely and regretful event of a release happening with a bug.
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- On your own fork, make a new branch `patch` based on `upstream/master`.
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- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
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- Fix the bug, and bump version (X.Y.Z+1).
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- A PR should be made on `master` from patch to directly this particular bug.
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- Open a pull-request from `patch` to `main`/`master` with the changes.
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## Getting help
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For further information/help, please consult the [nf-core/methylseq documentation](https://nf-co.re/methylseq/usage) and don't hesitate to get in touch on the nf-core Slack [#methylseq](https://nfcore.slack.com/channels/methylseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
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## Pipeline contribution conventions
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To make the nf-core/methylseq code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
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To make the `nf-core/methylseq` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
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### Adding a new step
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If you wish to contribute a new step, please use the following coding standards:
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1. Define the corresponding input channel into your new process from the expected previous process channel
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1. Define the corresponding input channel into your new process from the expected previous process channel.
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2. Write the process block (see below).
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3. Define the output channel if needed (see below).
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4. Add any new parameters to `nextflow.config` with a default (see below).
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### Default values
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Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
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Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
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Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
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‎.github/actions/nf-test-shard/action.yml‎

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name: "Get number of shards"
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description: "Get the number of nf-test shards for the current CI job"
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inputs:
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tags:
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description: "Tags to pass as argument for nf-test --tag parameter"
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required: true
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max_shards:
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description: "Maximum number of shards allowed"
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required: true
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outputs:
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shard:
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description: "Array of shard numbers"
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value: ${{ steps.shards.outputs.shard }}
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total_shards:
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description: "Total number of shards"
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value: ${{ steps.shards.outputs.total_shards }}
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runs:
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using: "composite"
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steps:
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- name: Install nf-test
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uses: nf-core/setup-nf-test@v1
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with:
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version: ${{ env.NFT_VER }}
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install-pdiff: true
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- name: Get number of shards
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id: shards
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shell: bash
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run: |
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# Run nf-test to get the number of related tests
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nftest_output=$(nf-test test --dry-run --changed-since HEAD^ --filter pipeline --tag ${{ inputs.tags }})
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echo "nf-test dry-run output: $nftest_output"
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# Default values for shard and total_shards
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shard="[]"
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total_shards=0
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# Check if there are related tests
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if echo "$nftest_output" | grep -q 'Nothing to do'; then
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echo "No related tests found."
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else
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# Extract the number of related tests
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number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p')
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if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then
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shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} ))
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shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .)
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total_shards="$shards_to_run"
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else
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echo "Unexpected output format. Falling back to default values."
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fi
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fi
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# Write to GitHub Actions outputs
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echo "shard=$shard" >> $GITHUB_OUTPUT
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echo "total_shards=$total_shards" >> $GITHUB_OUTPUT
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# Debugging output
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echo "Final shard array: $shard"
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echo "Total number of shards: $total_shards"

‎.github/actions/nf-test/action.yml‎

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name: "nf-test Action"
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description: "Runs nf-test with common setup steps"
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inputs:
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profile:
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description: "Profile to use"
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required: true
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shard:
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description: "Shard number for this CI job"
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required: true
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total_shards:
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description: "Total number of test shards(NOT the total number of matrix jobs)"
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required: true
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filters:
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description: "Filter test cases by specified types (e.g., module, pipeline, workflow or function)"
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required: true
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tags:
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description: "Tags to pass as argument for nf-test --tag parameter"
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required: true
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runs:
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using: "composite"
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steps:
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- uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
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with:
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distribution: "temurin"
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java-version: "17"
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- name: Setup Nextflow
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uses: nf-core/setup-nextflow@v2
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with:
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version: "${{ env.NXF_VER }}"
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- name: Set up Python
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uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
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with:
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python-version: "3.11"
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- name: Install nf-test
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uses: nf-core/setup-nf-test@v1
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with:
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version: "${{ env.NFT_VER }}"
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install-pdiff: true
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- name: Setup apptainer
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if: contains(inputs.profile, 'singularity')
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uses: eWaterCycle/setup-apptainer@main
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- name: Set up Singularity
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if: contains(inputs.profile, 'singularity')
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shell: bash
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run: |
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mkdir -p $NXF_SINGULARITY_CACHEDIR
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mkdir -p $NXF_SINGULARITY_LIBRARYDIR
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- name: Conda setup
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if: ${{inputs.profile == 'conda'}}
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uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
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with:
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auto-update-conda: true
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conda-solver: libmamba
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conda-remove-defaults: true
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- name: Run nf-test
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shell: bash
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run: |
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NFT_WORKDIR=~ \
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nf-test test \
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--ci \
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--shard ${{ inputs.shard }}/${{ inputs.total_shards }} \
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--changed-since HEAD^ \
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--profile=${{ inputs.profile }} \
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--filter ${{ inputs.filters }} \
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--tap=test.tap \
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--verbose \
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--tag ${{ inputs.tags }}
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# TODO If no test.tap, then make one to spoof?
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- uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
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if: ${{ inputs.path != '' }}
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with:
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path: >-
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test.tap
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- name: Clean up
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if: always()
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shell: bash
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run: |
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sudo rm -rf /home/ubuntu/tests/*

‎.github/workflows/awsfulltest.yml‎

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name: nf-core AWS full size tests
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# This workflow is triggered on PRs opened against the master branch.
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# This workflow is triggered on PRs opened against the main/master branch.
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# It can be additionally triggered manually with GitHub actions workflow dispatch button.
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# It runs the -profile 'test_full' on AWS batch
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on:
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branches:
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- main
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- master
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workflow_dispatch:
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pull_request_review:
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matrix:
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aligner: ["bismark", "bismark_hisat", "bwameth"]
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steps:
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- uses: octokit/request-action@v2.x
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- name: Get PR reviews
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uses: octokit/request-action@v2.x
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if: github.event_name != 'workflow_dispatch'
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id: check_approvals
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continue-on-error: true
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with:
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route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- id: test_variables
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- name: Check for approvals
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if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
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run: |
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echo "No review approvals found. At least 2 approvals are required to run this action automatically."
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exit 1
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- name: Check for enough approvals (>=2)
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id: test_variables
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if: github.event_name != 'workflow_dispatch'
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run: |
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JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
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CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
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test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
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- name: Launch workflow via Seqera Platform
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uses: seqeralabs/action-tower-launch@v2
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with:

‎.github/workflows/branch.yml‎

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name: nf-core branch protection
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# This workflow is triggered on PRs to master branch on the repository
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# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
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# This workflow is triggered on PRs to `main`/`master` branch on the repository
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# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
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on:
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branches: [master]
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branches:
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- main
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- master
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jobs:
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test:
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runs-on: ubuntu-latest
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steps:
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# PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
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# PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
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- name: Check PRs
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if: github.repository == 'nf-core/methylseq'
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run: |
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uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
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with:
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message: |
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## This PR is against the `master` branch :x:
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## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
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* Do not close this PR
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* Click _Edit_ and change the `base` to `dev`
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Hi @${{ github.event.pull_request.user.login }},
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It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
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The `master` branch on nf-core repositories should always contain code from the latest release.
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Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
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It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
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The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
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Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
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You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
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Note that even after this, the test will continue to show as failing until you push a new commit.

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