MultiQC-Additional overview stat table #677
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| name: nf-core CI | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFTEST_VER: "0.8.4" | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test_profile_standard: | |
| name: nf-test with standard profiles | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| profile: | |
| - "test" | |
| - "test_model_information" | |
| - "test_mouse_all_pep_lengths" | |
| - "test_assembly_only" | |
| - "test_bins_only" | |
| - "test_coassembly" | |
| - "test_mhcflurry" | |
| - "test_mhcnuggets_1" | |
| - "test_mhcnuggets_2" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Install nf-test | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Run nf-test | |
| run: | | |
| nf-test test --tag ${{ matrix.profile }} --profile ${{ matrix.profile }},docker --junitxml=test.xml --verbose | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v3 | |
| if: always() # always run even if the previous step fails | |
| with: | |
| report_paths: "*.xml" | |
| test_profile_download: | |
| name: nf-test with profiles needing entrez downloads | |
| # Only run on PRs from branches of nf-core/metapep repository or on push if this is the nf-core dev branch (merged PRs) | |
| # (GitHub secrets are not accessible for workflows from forks) | |
| if: "${{ github.event.pull_request.head.repo.full_name == 'nf-core/metapep' || (github.event_name == 'push' && github.repository == 'nf-core/metapep') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| profile: | |
| - "test_all" | |
| - "test_mouse" | |
| - "test_taxa_only" | |
| - "test_taxa_specific_assembly" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Install nf-test | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Run nf-test | |
| env: | |
| NCBI_EMAIL: ${{ secrets.NCBI_EMAIL }} | |
| NCBI_KEY: ${{ secrets.NCBI_KEY }} | |
| run: | | |
| nextflow secrets set NCBI_EMAIL ${{ secrets.NCBI_EMAIL }} | |
| nextflow secrets set NCBI_KEY ${{ secrets.NCBI_KEY }} | |
| nf-test test --tag ${{ matrix.profile }} --profile ${{ matrix.profile }},docker --junitxml=test.xml --verbose | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v3 | |
| if: always() # always run even if the previous step fails | |
| with: | |
| report_paths: "*.xml" |