Update diann_convert.py #14
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
| 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 | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| env: | |
| NXF_ANSI_LOG: false | |
| CAPSULE_LOG: none | |
| TEST_PROFILE: ${{ matrix.test_profile }} | |
| EXEC_PROFILE: ${{ matrix.exec_profile }} | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/quantms') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # Nextflow versions | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| test_profile: ["test_lfq", "test_lfq_sage", "test_dia", "test_localize", "test_tmt"] | |
| exec_profile: ["docker", "conda"] | |
| exclude: | |
| - test_profile: test_dia | |
| exec_profile: conda | |
| - test_profile: test_localize | |
| exec_profile: conda | |
| - NXF_VER: "latest-everything" | |
| exec_profile: "conda" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Install micromamba | |
| if: matrix.exec_profile == 'conda' | |
| run: | | |
| wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba | |
| echo "$(pwd)/bin" >> $GITHUB_PATH | |
| echo "$(pwd)/micromamba/bin" >> $GITHUB_PATH | |
| ./bin/micromamba shell init -s bash -p ./micromamba | |
| echo $'channels:\n - conda-forge\n - bioconda\n - defaults\nuse_lockfiles: false' >> ~/.mambarc | |
| - name: Run pipeline with test data | |
| if: matrix.exec_profile != 'conda' | |
| # 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 $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results | |
| - name: Run pipeline with test data in conda profile (and single-threaded) | |
| if: matrix.exec_profile == 'conda' | |
| # 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_PROFILE,micromamba --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results | |
| - name: Gather failed logs | |
| if: failure() || cancelled() | |
| run: | | |
| mkdir failed_logs | |
| failed=$(grep "FAILED" ${TEST_PROFILE}_${EXEC_PROFILE}_results/pipeline_info/execution_trace.txt | cut -f 2) | |
| while read -r line ; do cp $(ls work/${line}*/*.log) failed_logs/ | true ; done <<< "$failed" | |
| - uses: actions/upload-artifact@v1 | |
| if: failure() || cancelled() | |
| name: Upload failed logs | |
| with: | |
| name: failed_logs | |
| path: failed_logs | |
| - uses: actions/upload-artifact@v1 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: ${{ env.TEST_PROFILE }}_${{ env.EXEC_PROFILE }}_results | |
| path: ${{ env.TEST_PROFILE }}_${{ env.EXEC_PROFILE }}_results | |
| - uses: actions/upload-artifact@v1 | |
| if: always() | |
| name: Upload log | |
| with: | |
| name: nextflow.log | |
| path: .nextflow.log |