Trying to remove bioconda default channel #60
Workflow file for this run
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| name: Run tests | |
| on: | |
| pull_request: | |
| branches: [main] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # 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@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4 | |
| with: | |
| node-version: "20" | |
| - name: Install Prettier | |
| run: npm install -g prettier@3.1.0 | |
| - name: Run Prettier --check | |
| run: prettier --check . | |
| editorconfig: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # 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: gallvp/detect-nf-test-changes@a42129de36ec0491bb2ffdd0e041923d27b09dac # master | |
| with: | |
| head: ${{ github.sha }} | |
| base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }} | |
| n_parents: 2 | |
| ignored: "nf-core-modules/**" | |
| log_level: "DEBUG" | |
| - name: Separate modules and subworkflows | |
| id: outputs | |
| run: | | |
| echo modules=$(echo '${{ steps.list.outputs.components }}' | jq -c '. | map(select(contains("modules/gallvp/"))) | map(gsub("modules/gallvp/"; ""))') >> $GITHUB_OUTPUT | |
| echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows/gallvp/"))) | map(gsub("subworkflows/gallvp/"; ""))') >> $GITHUB_OUTPUT | |
| - name: debug | |
| run: | | |
| echo ${{ steps.list.outputs.components }} | |
| 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@39cd14951b08e74b54015e9e001cdefcf80e669f # 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 -g https://github.com/GallVp/nxf-components.git 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@39cd14951b08e74b54015e9e001cdefcf80e669f # 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 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] | |
| exclude: | |
| - profile: conda | |
| path: modules/gallvp/braker3 | |
| - profile: conda | |
| path: modules/gallvp/edta/edta | |
| - profile: conda | |
| path: subworkflows/gallvp/fasta_edta_lai | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFTEST_VER: "0.9.0" | |
| 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' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Set up Python | |
| uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # 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 | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda,defaults | |
| - name: Conda setup | |
| if: matrix.profile == 'conda' | |
| 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: | |
| [pre-commit, 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) }}" |