update reports #27
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
| name: Test Harpy Modules | |
| on: | |
| push: | |
| branches: | |
| - 'dev' | |
| pull_request: | |
| branches: | |
| - dev | |
| # Cancel in progress workflows on pull_requests. | |
| # https://docs.github.com/en/actions/using-jobs/using-concurrency#example-using-a-fallback-value | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }} | |
| cancel-in-progress: true | |
| env: | |
| CACHE_NUMBER: 0 # increase to reset cache manually | |
| jobs: | |
| changes: | |
| name: detect file changes | |
| runs-on: ubuntu-latest | |
| # Required permissions | |
| permissions: | |
| pull-requests: read | |
| # Set job outputs to values from filter step | |
| outputs: | |
| preflight: ${{ steps.filter.outputs.qc }} | |
| demux: ${{ steps.filter.outputs.demux }} | |
| qc: ${{ steps.filter.outputs.qc }} | |
| bwa: ${{ steps.filter.outputs.bwa }} | |
| ema: ${{ steps.filter.outputs.ema }} | |
| minimap: ${{ steps.filter.outputs.minimap }} | |
| mpileup: ${{ steps.filter.outputs.mpileup }} | |
| freebayes: ${{ steps.filter.outputs.freebayes }} | |
| leviathan: ${{ steps.filter.outputs.leviathan }} | |
| naibr: ${{ steps.filter.outputs.naibr }} | |
| impute: ${{ steps.filter.outputs.impute }} | |
| phase: ${{ steps.filter.outputs.phase }} | |
| simvars: ${{ steps.filter.outputs.simvars }} | |
| simreads: ${{ steps.filter.outputs.simreads }} | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| - name: check which files changed | |
| uses: dorny/paths-filter@v3 | |
| id: filter | |
| with: | |
| base: 'dev' | |
| filters: .github/filters.yml | |
| pkgbuild: | |
| name: harpy installation | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| test_dmux_gen1: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.demux == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test demux gen1 | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: harpy demultiplex | |
| run: harpy demultiplex gen1 --samplesheet test/demux/samples.schema test/demux/Undetermined_S0_L004_I1_001.fastq.gz | |
| shell: micromamba-shell {0} | |
| test_qc: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.qc == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test qc | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| env: | |
| ACTIONS_STEP_DEBUG: true | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| log-level: error | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: harpy qc | |
| shell: micromamba-shell {0} | |
| run: harpy qc -x "--trim_poly_g" -s "--show-failed-logs" test/fastq | |
| - name: harpy qc skip adapter trimming | |
| if: always() | |
| shell: micromamba-shell {0} | |
| run: harpy qc -a -s "--show-failed-logs" test/fastq | |
| test_bwa: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.bwa == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test align BWA | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| env: | |
| ACTIONS_STEP_DEBUG: true | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| log-level: error | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: test bwa | |
| shell: micromamba-shell {0} | |
| run: harpy align bwa -g test/genome/genome.fasta.gz -s "--show-failed-logs" -x "-A 2" test/fastq | |
| test_ema: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.ema == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test align EMA | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| env: | |
| ACTIONS_STEP_DEBUG: true | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| log-level: error | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: test ema | |
| shell: micromamba-shell {0} | |
| run: harpy align ema --ema-bins 150 -g test/genome/genome.fasta.gz -s "--show-failed-logs" -x "-d" test/fastq | |
| test_minimap: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.minimap == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test align minimap | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| env: | |
| ACTIONS_STEP_DEBUG: true | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| log-level: error | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: test minimap | |
| shell: micromamba-shell {0} | |
| run: harpy align minimap -g test/genome/genome.fasta.gz -s "--show-failed-logs" -x "--seed 13" test/fastq | |
| test_impute: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.impute == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test impute | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| env: | |
| ACTIONS_STEP_DEBUG: true | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| log-level: error | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: impute | |
| shell: micromamba-shell {0} | |
| run: harpy impute --vcf test/vcf/test.bcf -p test/stitch.params -s "--show-failed-logs" test/bam | |
| - name: impute from vcf | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: harpy impute --vcf-samples -o vcfImpute --vcf test/vcf/test.bcf -p test/stitch.params -s "--show-failed-logs" test/bam | |
| test_phase: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.phase == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test phase | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| env: | |
| ACTIONS_STEP_DEBUG: true | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| log-level: error | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: phase | |
| shell: micromamba-shell {0} | |
| run: harpy phase --vcf test/vcf/test.bcf -s "--show-failed-logs" -x "--max_iter 10001" test/bam | |
| - name: phase with indels | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: harpy phase --vcf test/vcf/test.bcf -o phaseindel -g test/genome/genome.fasta.gz -s "--show-failed-logs" test/bam | |
| - name: phase from vcf | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: harpy phase --vcf-samples -o phasevcf --vcf test/vcf/test.bcf -s "--show-failed-logs" test/bam | |
| test_leviathan: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.leviathan == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test sv leviathan | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| env: | |
| ACTIONS_STEP_DEBUG: true | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| log-level: error | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: leviathan | |
| shell: micromamba-shell {0} | |
| run: harpy sv leviathan -n 100 -b 1 -g test/genome/genome.fasta.gz -q -s "--show-failed-logs" -x "-M 2002" test/bam | |
| continue-on-error: true | |
| - name: leviathan-pop | |
| if: always() | |
| shell: micromamba-shell {0} | |
| run: harpy sv leviathan -n 100 -b 1 -g test/genome/genome.fasta.gz -o SV/leviathanpop -p test/samples.groups -q -s "--show-failed-logs" test/bam | |
| test_naibr: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.leviathan == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test sv naibr | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| env: | |
| ACTIONS_STEP_DEBUG: true | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| log-level: error | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: naibr | |
| shell: micromamba-shell {0} | |
| run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/naibr -s "--show-failed-logs" -x "-min_sv 5000" test/bam_phased && rm -r Genome | |
| - name: naibr pop | |
| if: always() | |
| shell: micromamba-shell {0} | |
| run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/pop -p test/samples.groups -s "--show-failed-logs" test/bam_phased && rm -r Genome | |
| - name: naibr with phasing | |
| if: always() | |
| shell: micromamba-shell {0} | |
| run: | | |
| harpy sv naibr -g test/genome/genome.fasta.gz -o SV/phase -v test/vcf/test.phased.bcf -s "--show-failed-logs" test/bam && rm -r Genome | |
| - name: naibr pop with phasing | |
| if: always() | |
| shell: micromamba-shell {0} | |
| run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/phasepop -v test/vcf/test.phased.bcf -p test/samples.groups -s "--show-failed-logs" test/bam && rm -r Genome | |
| test_simulate_variants: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.simvars == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test simulate variants | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| env: | |
| ACTIONS_STEP_DEBUG: true | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| log-level: error | |
| - name: Install harpy | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| shell: micromamba-shell {0} | |
| - name: simulate random snps/indels | |
| shell: micromamba-shell {0} | |
| run: | | |
| harpy simulate snpindel --snp-count 10 --indel-count 10 -z 0.5 -s "--show-failed-logs" test/genome/genome.fasta.gz | |
| harpy simulate snpindel --prefix Simulate/snpvcf --snp-vcf Simulate/snpindel/sim.snpindel.snp.hap1.vcf --indel-vcf Simulate/snpindel/sim.snpindel.indel.hap1.vcf -s "--show-failed-logs" test/genome/genome.fasta.gz | |
| - name: simulate inversions | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: | | |
| harpy simulate inversion --count 10 -z 0.5 test/genome/genome.fasta.gz | |
| harpy simulate inversion --prefix Simulate/invvcf --vcf Simulate/inversion/sim.inversion.hap1.vcf -s "--show-failed-logs" test/genome/genome.fasta.gz | |
| - name: simulate cnv | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: | | |
| harpy simulate cnv --count 10 -z 0.5 test/genome/genome.fasta.gz | |
| harpy simulate cnv --prefix Simulate/cnvvcf --vcf Simulate/cnv/sim.cnv.hap1.vcf -s "--show-failed-logs" test/genome/genome.fasta.gz | |
| - name: simulate translocations | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: | | |
| harpy simulate translocation --count 10 -z 0.5 test/genome/genome.fasta.gz | |
| harpy simulate translocation --prefix Simulate/transvcf --vcf Simulate/translocation/sim.translocation.hap1.vcf -s "--show-failed-logs" test/genome/genome.fasta.gz | |
| test_simulate_linkedreads: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.simreads == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test simulate linkedreads | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| env: | |
| ACTIONS_STEP_DEBUG: true | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| log-level: error | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: simulate linked reads | |
| shell: micromamba-shell {0} | |
| run: harpy simulate linkedreads -s "--show-failed-logs" -t 4 -n 2 -l 100 -p 50 test/genome/genome.fasta.gz test/genome/genome2.fasta.gz | |
| test_extras: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.extras == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: test harpy extras | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| env: | |
| ACTIONS_STEP_DEBUG: true | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| log-level: error | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: harpy stitchparams | |
| shell: micromamba-shell {0} | |
| run: harpy stitchparams -o params.file | |
| - name: harpy popgroup | |
| shell: micromamba-shell {0} | |
| run: harpy popgroup test/fastq |