diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index a36977c177ff..c3b65b104558 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -19,23 +19,11 @@ env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} jobs: - pre-commit: + lint: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v3 - - uses: pre-commit/action@v3.0.0 - # 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@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 - name: Install NodeJS uses: actions/setup-node@v4 @@ -45,30 +33,29 @@ jobs: - name: Install Prettier run: npm install -g prettier - - name: Run Prettier --check - run: prettier --check . - - editorconfig: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 + - name: Install editorconfig-checker + run: npm install -g editorconfig-checker - - uses: actions/setup-node@v4 + - uses: pre-commit/action@v3.0.0 + # 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: - node-version: "20" + extra_args: "" - - name: Install editorconfig-checker - run: npm install -g editorconfig-checker + - name: Run Prettier --check + run: prettier --check . - name: Run ECLint check run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) - pytest-changes: - name: pytest-changes + changes: + name: changes runs-on: ubuntu-latest outputs: # Expose matched filters as job 'modules' output variable - modules: ${{ steps.filter.outputs.changes }} + pytest-modules: ${{ steps.pytest-filter.outputs.changes }} + nf-test-modules: ${{ steps.nf-test-filter.outputs.changes }} steps: - uses: actions/checkout@v4 with: @@ -76,22 +63,11 @@ jobs: # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented - uses: mirpedrol/paths-filter@main - id: filter + id: pytest-filter with: filters: "tests/config/pytest_modules.yml" token: "" - nf-test-changes: - name: nf-test-changes - runs-on: ubuntu-latest - outputs: - # Expose matched filters as job 'modules' output variable - modules: ${{ steps.filter.outputs.changes }} - steps: - - uses: actions/checkout@v4 - with: - fetch-depth: 2 # To retrieve the preceding commit. - - name: Combine all tags.yml files id: get_tags run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml @@ -101,7 +77,7 @@ jobs: # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented - uses: mirpedrol/paths-filter@main - id: filter + id: nf-test-filter with: filters: ".github/tags.yml" token: "" @@ -109,15 +85,15 @@ jobs: nf-core-lint: runs-on: ubuntu-latest name: nf-core-lint - needs: [pytest-changes, nf-test-changes] - if: ${{ (needs.pytest-changes.outputs.modules != '[]') || (needs.nf-test-changes.outputs.modules != '[]') }} + needs: [changes] + if: ${{ (needs.changes.outputs.pytest-modules != '[]') || (needs.changes.outputs.nf-test-modules != '[]') }} strategy: fail-fast: false matrix: tags: [ - "${{ fromJson(needs.pytest-changes.outputs.modules) }}", - "${{ fromJson(needs.nf-test-changes.outputs.modules) }}", + "${{ fromJson(needs.changes.outputs.nf-test-modules) }}", + "${{ fromJson(needs.changes.outputs.nf-test-modules) }}", ] steps: - uses: actions/checkout@v4 @@ -162,12 +138,12 @@ jobs: pytest: runs-on: ubuntu-latest name: pytest - needs: [pytest-changes] - if: needs.pytest-changes.outputs.modules != '[]' + needs: [changes] + if: needs.changes.outputs.pytest-modules != '[]' strategy: fail-fast: false matrix: - tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"] + tags: ["${{ fromJson(needs.changes.outputs.pytest-modules) }}"] profile: ["docker", "singularity", "conda"] exclude: - tags: "nf-test" @@ -441,12 +417,12 @@ jobs: nf-test: runs-on: ubuntu-latest name: nf-test - needs: [nf-test-changes] - if: needs.nf-test-changes.outputs.modules != '[]' + needs: [changes] + if: needs.changes.outputs.nf-test-modules != '[]' strategy: fail-fast: false matrix: - tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"] + tags: ["${{ fromJson(needs.changes.outputs.nf-test-modules) }}"] profile: ["docker", "singularity", "conda"] exclude: - tags: "nf-test" @@ -607,7 +583,7 @@ jobs: confirm-pass: runs-on: ubuntu-latest - needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test] + needs: [lint, nf-core-lint, pytest, nf-test] if: always() steps: - name: All tests ok diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 50e59f2b8cc0..eed6945a6869 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -30,6 +30,8 @@ process FASTQC { [ -f "\${new_name}" ] || ln -s \$old_name \$new_name done + # I'm a fake change. + fastqc \\ $args \\ --threads $task.cpus \\