rm comments #9
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| 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.dmux }} | |
| 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 }} | |
| simvar: ${{ steps.filter.outputs.simvar }} | |
| simreads: ${{ steps.filter.outputs.simreads }} | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| - 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.dmux == '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 |