Replace missing GTF gene_names with IDs #963
Workflow file for this run
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| name: 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 | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| 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 == 'qbic-pipelines/rnadeseq') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # Nextflow versions | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Check if Dockerfile or Conda environment changed | |
| uses: technote-space/get-diff-action@v4 | |
| with: | |
| FILES: | | |
| Dockerfile | |
| environment.yml | |
| - name: Build new docker image | |
| if: env.MATCHED_FILES | |
| run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:dev | |
| - name: Pull docker image | |
| if: ${{ !env.MATCHED_FILES }} | |
| run: | | |
| docker pull ghcr.io/qbic-pipelines/rnadeseq:dev | |
| docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:dev | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run pipeline with test data | |
| run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker | |
| parameters: | |
| name: Test workflow parameters | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: "23.04.0" | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| # This tells github to continue running other profile tests if some tests fail (default cancels all tests upon failure) | |
| fail-fast: false | |
| matrix: | |
| config: | |
| [ | |
| "test", | |
| "test_full", | |
| "test_contrast_matrix", | |
| "test_contrast_list", | |
| "test_no_multiqc", | |
| "test_relevel", | |
| "test_smrnaseq", | |
| "test_star_rsem", | |
| "test_star_salmon", | |
| "test_use_vst", | |
| "test_batcheffect", | |
| "test_custom_gmt", | |
| ] | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Check if Dockerfile or Conda environment changed | |
| uses: technote-space/get-diff-action@v4 | |
| with: | |
| FILES: | | |
| Dockerfile | |
| environment.yml | |
| - name: Build new docker image | |
| if: env.MATCHED_FILES | |
| run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:dev | |
| - name: Pull docker image | |
| if: ${{ !env.MATCHED_FILES }} | |
| run: | | |
| docker pull ghcr.io/qbic-pipelines/rnadeseq:dev | |
| docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:dev | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.x" | |
| - name: Install dependencies | |
| run: python -m pip install --upgrade pip pytest-workflow | |
| - name: Run pipeline with tests settings | |
| uses: Wandalen/wretry.action@v1.0.11 | |
| with: | |
| command: pytest --tag ${{ matrix.config }} --kwdof --git-aware --color=yes | |
| attempt_limit: 3 | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always /tmp/pytest_workflow_*/*/log.{out,err} | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: logs-${{ matrix.profile }} | |
| path: | | |
| /tmp/pytest_workflow_*/*/.nextflow.log | |
| /tmp/pytest_workflow_*/*/log.out | |
| /tmp/pytest_workflow_*/*/log.err | |
| /tmp/pytest_workflow_*/*/work | |
| !/tmp/pytest_workflow_*/*/work/conda | |
| !/tmp/pytest_workflow_*/*/work/singularity | |
| /tmp/pytest_workflow_*/**/.command.log |