Merge pull request #1 from mirpedrol/msa-modules-subset

Subset nf-core/modules repo

.github/workflows/fix-linting.yml

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+name: fix-linting
+run-name: fix linting (automated)
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  fix-linting:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
+      github.repository == 'nf-core/modules'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
+      - uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
+
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
+
+      # Check that we actually need to fix something
+      - name: Run 'prettier --check'
+        id: prettier_status
+        run: |
+          if prettier --check ${GITHUB_WORKSPACE}; then
+            echo "::set-output name=result::pass"
+          else
+            echo "::set-output name=result::fail"
+          fi
+      - name: Run 'prettier --write'
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: prettier --write ${GITHUB_WORKSPACE}
+
+      - name: Post nothing-to-do comment
+        if: steps.prettier_status.outputs.result == 'pass'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          issue-number: ${{ github.event.issue.number }}
+          body: |
+            Nothing for me to do here! :shrug:
+            This is probably because the linting errors come from `nf-core lint` and have to be fixed manually (or with `nf-core lint --fix`).
+
+      - name: Commit & push changes
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: |
+          git config user.email "[email protected]"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Fix linting with Prettier"
+          git push

.github/workflows/test.yml

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+name: Run tests
+on:
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
+        # FIXME Flip this off once we get to less than a couple hundred. Adding
+        # this so it will only run against changed files. It'll make it much
+        # easier to fix these as they come up rather than everything at once.
+        with:
+          extra_args: ""
+
+  prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+      - name: Install NodeJS
+        uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
+        with:
+          node-version: "20"
+
+      - name: Install Prettier
+        run: npm install -g [email protected]
+
+      - name: Run Prettier --check
+        run: prettier --check .
+
+  editorconfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+      - uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
+        with:
+          node-version: "20"
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
+
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose detected tags as 'modules' and 'workflows' output variables
+      paths: ${{ steps.list.outputs.components }}
+      modules: ${{ steps.outputs.outputs.modules }}
+      subworkflows: ${{ steps.outputs.outputs.subworkflows}}
+      # Prod for version bumping
+
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+        with:
+          fetch-depth: 0
+
+      - name: List nf-test files
+        id: list
+        uses: adamrtalbot/detect-nf-test-changes@6e67b7a6bd3caf8571b99cab3ab764c0e758f55c # v0.0.3
+        with:
+          head: ${{ github.sha }}
+          base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }}
+          n_parents: 2
+
+      - name: Separate modules and subworkflows
+        id: outputs
+        run: |
+          echo modules=$(echo '${{ steps.list.outputs.components }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/class-modules/"; ""))') >> $GITHUB_OUTPUT
+          echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows"))) | map(gsub("subworkflows/class-modules/"; ""))') >> $GITHUB_OUTPUT
+
+      - name: debug
+        run: |
+          echo ${{ steps.outputs.outputs.modules }}
+          echo ${{ steps.outputs.outputs.subworkflows }}
+
+  nf-core-lint-modules:
+    runs-on: ubuntu-latest
+    name: nf-core-lint-modules
+    needs: nf-test-changes
+    if: ( needs.nf-test-changes.outputs.modules != '[]')
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"]
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+      - name: Set up Python
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: "3.11"
+
+      - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+        id: cache-pip
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip
+          restore-keys: |
+            ${{ runner.os }}-pip
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Lint module ${{ matrix.tags }}
+        run: nf-core modules --git-remote https://github.com/mirpedrol/class-modules lint ${{ matrix.tags }}
+
+  nf-core-lint-subworkflows:
+    runs-on: ubuntu-latest
+    name: nf-core-lint-modules
+    needs: nf-test-changes
+    if: ( needs.nf-test-changes.outputs.subworkflows != '[]')
+    strategy:
+      fail-fast: false
+      matrix:
+        tags:
+          [
+            "${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}",
+          ]
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+      - name: Set up Python
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: "3.11"
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Lint module ${{ matrix.tags }}
+        run: nf-core subworkflows --git-remote https://github.com/mirpedrol/class-modules lint ${{ matrix.tags }}
+
+  nf-test:
+    runs-on: ubuntu-latest
+    name: nf-test
+    needs: nf-test-changes
+    if: ( needs.nf-test-changes.outputs.paths != '[]' )
+    strategy:
+      fail-fast: false
+      matrix:
+        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
+        profile: [conda, docker, singularity]
+    env:
+      NXF_ANSI_LOG: false
+      NFTEST_VER: "0.8.4"
+
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+      - uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+
+      - name: Setup apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Set up Python
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: "3.11"
+      - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+        id: cache-pip-pdiff
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-pdiff
+          restore-keys: |
+            ${{ runner.os }}-pip-pdiff
+
+      - name: Install Python dependencies
+        run: python -m pip install --upgrade pip pdiff cryptography
+
+      - name: Set up miniconda
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+
+      - name: Conda setup
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      # Test the module
+      - name: Run nf-test
+        env:
+          NFT_DIFF: "pdiff"
+          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
+        run: |
+          PROFILE=${{ matrix.profile }}
+
+          NFT_WORKDIR=~ \
+          nf-test test \
+            --profile=${{ matrix.profile }} \
+            --tap=test.tap \
+            --verbose \
+            ${{ matrix.path }}
+
+      - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
+        with:
+          path: >-
+            test.tap
+
+      - name: Clean up
+        if: always()
+        run: |
+          sudo rm -rf /home/ubuntu/tests/
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs:
+      [
+        prettier,
+        editorconfig,
+        nf-core-lint-modules,
+        nf-core-lint-subworkflows,
+        nf-test-changes,
+        nf-test,
+      ]
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - [email protected]
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.28.5
+    hooks:
+      - id: check-jsonschema
+        # match meta.ymls in one of the subdirectories of modules/nf-core
+        files: ^modules/nf-core/.*/meta\.yml$
+        args: ["--schemafile", "modules/yaml-schema.json"]
+      - id: check-jsonschema
+        # match meta.ymls in one of the subdirectories of subworkflows/nf-core
+        files: ^subworkflows/nf-core/.*/meta\.yml$
+        args: ["--schemafile", "subworkflows/yaml-schema.json"]
+      - id: check-github-workflows
+  - repo: https://github.com/renovatebot/pre-commit-hooks
+    rev: 37.408.2
+    hooks:
+      - id: renovate-config-validator
+  # use ruff for python files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.10
+    hooks:
+      - id: ruff
+        files: \.py$
+        args: [--fix, --exit-non-zero-on-fix, "--select", "I,E1,E4,E7,E9,F,UP,N"] # sort imports and fix (rules taken from nf-core/tools)
+      - id: ruff-format # formatter