name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: push: branches: - dev pull_request: release: types: [published] env: NXF_ANSI_LOG: false CAPSULE_LOG: none jobs: test: name: Run pipeline with test data # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}" runs-on: ubuntu-latest strategy: matrix: # Nextflow versions include: # Test pipeline minimum Nextflow version - NXF_VER: "21.10.3" NXF_EDGE: "" # Test latest edge release of Nextflow - NXF_VER: "" NXF_EDGE: "1" parameters: - "--perform_longread_clip false" - "--perform_shortread_clipmerge false" - "--shortread_clipmerge_tool fastp" - "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged" - "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs" - "--shortread_clipmerge_tool adapterremoval" - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged" - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs" - "--shortread_complexityfilter_tool bbduk" - "--shortread_complexityfilter_tool prinseq" - "--perform_runmerging" - "--perform_runmerging --shortread_clipmerge_mergepairs" - "--shortread_complexityfilter false --perform_shortread_hostremoval" steps: - name: Check out pipeline code uses: actions/checkout@v2 - name: Install Nextflow env: NXF_VER: ${{ matrix.NXF_VER }} # Uncomment only if the edge release is more recent than the latest stable release # See https://github.com/nextflow-io/nextflow/issues/2467 # NXF_EDGE: ${{ matrix.NXF_EDGE }} run: | wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - name: Show current locale run: locale - name: Set UTF-8 enabled locale run: | sudo locale-gen en_US.UTF-8 sudo update-locale LANG=en_US.UTF-8 - name: Run pipeline with test data # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} #