Update README.md #121
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: | |
| - 'main' | |
| pull_request: | |
| branches: | |
| - main | |
| # 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.preflight }} | |
| 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 }} | |
| other: ${{ steps.filter.outputs.other }} | |
| container: ${{ steps.filter.outputs.container }} | |
| modules: ${{ steps.filter.outputs.modules }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Check Which Files Have Changes | |
| uses: dorny/paths-filter@v3 | |
| id: filter | |
| with: | |
| base: 'main' | |
| filters: .github/filters.yml | |
| pkgbuild: | |
| needs: changes | |
| name: Build/Cache Container | |
| 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache | |
| - name: Rebuild Dockerfile | |
| id: rebuild | |
| if: ${{ needs.changes.outputs.container == 'true' }} | |
| shell: micromamba-shell {0} | |
| run: harpy containerize | |
| - name: Set up Docker Buildx | |
| id: buildx | |
| if: ${{ steps.rebuild.outcome == 'success' }} | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Login to Docker Hub | |
| id: dockerhub | |
| if: ${{ steps.buildx.outcome == 'success' }} | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and Push to Dockerhub | |
| if: ${{ steps.dockerhub.outcome == 'success' }} | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| push: true | |
| tags: pdimens/harpy:latest | |
| - name: Pull Image Locally | |
| id: singularity | |
| shell: micromamba-shell {0} | |
| if: ${{ needs.changes.outputs.modules == 'true' }} | |
| run: harpy qc --skipreports -a test/fastq/sample1.*.fq.gz | |
| - name: Create Singularity Artifact | |
| if: ${{ steps.singularity.outcome == 'success' }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity/*.simg | |
| retention-days: 1 | |
| dmux_gen1: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.demux == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: harpy demultiplex | |
| shell: micromamba-shell {0} | |
| run: harpy demultiplex gen1 --schema test/demux/samples.schema test/demux/Undetermined_S0_L004_R* test/demux/Undetermined_S0_L004_I* | |
| preflight: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.preflight == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: preflight | |
| 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: test preflight fastq | |
| shell: micromamba-shell {0} | |
| run: harpy preflight fastq test/fastq | |
| - name: test preflight bam | |
| if: always() | |
| shell: micromamba-shell {0} | |
| run: harpy preflight bam test/bam | |
| qc: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.qc == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: harpy qc | |
| shell: micromamba-shell {0} | |
| run: harpy qc -x "--trim_poly_g" --snakemake "--show-failed-logs" test/fastq | |
| - name: harpy qc skip adapter trimming | |
| if: always() | |
| shell: micromamba-shell {0} | |
| run: harpy qc -a --snakemake "--show-failed-logs" test/fastq | |
| bwa: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.bwa == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: test bwa | |
| shell: micromamba-shell {0} | |
| run: harpy align bwa -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs" -x "-A 2" test/fastq | |
| ema: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.ema == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: test ema | |
| shell: micromamba-shell {0} | |
| run: harpy align ema --ema-bins 150 -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs" -x "-d" test/fastq | |
| minimap: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.minimap == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: test minimap | |
| shell: micromamba-shell {0} | |
| run: harpy align minimap -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs" -x "--seed 13" test/fastq | |
| mpileup: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.mpileup == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: mpileup | |
| 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: snp mpileup | |
| shell: micromamba-shell {0} | |
| run: harpy snp mpileup -r test/positions.bed -g test/genome/genome.fasta.gz -x "--ignore-RG" test/bam | |
| - name: snp mpileup-pop | |
| shell: micromamba-shell {0} | |
| run: harpy snp mpileup -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups --snakemake "--show-failed-logs" test/bam | |
| freebayes: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.freebayes == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: freebayes | |
| 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: snp freebayes | |
| shell: micromamba-shell {0} | |
| run: harpy snp freebayes -r test/positions.bed -g test/genome/genome.fasta.gz -x "-g 200" test/bam | |
| - name: snp freebayes-pop | |
| shell: micromamba-shell {0} | |
| run: harpy snp freebayes -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups --snakemake "--show-failed-logs" test/bam | |
| impute: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.impute == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: impute | |
| shell: micromamba-shell {0} | |
| run: harpy impute --vcf test/vcf/test.bcf -p test/stitch.params --snakemake "--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 --snakemake "--show-failed-logs" test/bam | |
| phase: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.phase == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: phase | |
| shell: micromamba-shell {0} | |
| run: harpy phase --vcf test/vcf/test.bcf --snakemake "--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 --snakemake "--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 --snakemake "--show-failed-logs" test/bam | |
| leviathan: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.leviathan == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: leviathan | |
| shell: micromamba-shell {0} | |
| run: harpy sv leviathan -n 100 -b 1 -g test/genome/genome.fasta.gz --snakemake "--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 --snakemake "--show-failed-logs" test/bam | |
| naibr: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.naibr == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: naibr | |
| shell: micromamba-shell {0} | |
| run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/naibr --snakemake "--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 --snakemake "--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 --snakemake "--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 --snakemake "--show-failed-logs" test/bam && rm -r Genome | |
| simulate_variants: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.simvars == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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 | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: simulate random snps/indels | |
| shell: micromamba-shell {0} | |
| run: | | |
| harpy simulate snpindel --snp-count 10 --indel-count 10 -z 0.5 --snakemake "--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 --snakemake "--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 --snakemake "--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 --snakemake "--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 --snakemake "--show-failed-logs" test/genome/genome.fasta.gz | |
| simulate_linkedreads: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.simreads == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: simulate linked reads | |
| shell: micromamba-shell {0} | |
| run: harpy simulate linkedreads --snakemake "--show-failed-logs" -t 4 -n 2 -l 100 -p 50 test/genome/genome.fasta.gz test/genome/genome2.fasta.gz | |
| extras: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.other == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: 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: Clear Space | |
| run: rm -rf /opt/hostedtoolcache && mkdir -p .snakemake/singularity | |
| - 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 |