haplotagging barcodes as default #417
Workflow file for this run
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| 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 }} | |
| deconvolve: ${{ steps.filter.outputs.deconvolve }} | |
| demux: ${{ steps.filter.outputs.demux }} | |
| qc: ${{ steps.filter.outputs.qc }} | |
| bwa: ${{ steps.filter.outputs.bwa }} | |
| ema: ${{ steps.filter.outputs.ema }} | |
| strobealign: ${{ steps.filter.outputs.strobealign }} | |
| 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 }} | |
| assembly: ${{ steps.filter.outputs.assembly }} | |
| 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 --skip-reports --quiet 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet --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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 "--low_complexity_filter" --quiet test/fastq | |
| - name: harpy qc all options | |
| shell: micromamba-shell {0} | |
| run: harpy qc -a -d -c 21,40,3,0 --quiet test/fastq | |
| deconvolve: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.deconvolve == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: deconvolve | |
| 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: harpy deconvolve | |
| shell: micromamba-shell {0} | |
| run: harpy deconvolve --quiet 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet -g test/genome/genome.fasta.gz -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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet --ema-bins 150 -g test/genome/genome.fasta.gz test/fastq | |
| strobe: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.strobealign == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: align strobe | |
| 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: test strobealign | |
| shell: micromamba-shell {0} | |
| run: harpy align strobe --quiet -l 125 -g test/genome/genome.fasta.gz 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet -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 --quiet -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet -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 --quiet -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet --vcf test/vcf/test.bcf -p test/stitch.params test/bam | |
| - name: impute from vcf | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: harpy impute --quiet --vcf-samples -o vcfImpute --vcf test/vcf/test.bcf -p test/stitch.params 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet --vcf test/vcf/test.bcf -x "--max_iter 10001" test/bam | |
| - name: phase with indels | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: harpy phase --quiet --vcf test/vcf/test.bcf -o phaseindel -g test/genome/genome.fasta.gz test/bam | |
| - name: phase from vcf | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: | | |
| cp test/bam/sample1.bam test/bam/pineapple.bam && rename_bam.py -d pineapple1 test/bam/pineapple.bam | |
| harpy phase --quiet --vcf-samples -o phasevcf --vcf test/vcf/test.bcf 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet -s 100 -b 1 -g test/genome/genome.fasta.gz -x "-M 2002" test/bam | |
| continue-on-error: true | |
| - name: leviathan-pop | |
| if: always() | |
| shell: micromamba-shell {0} | |
| run: harpy sv leviathan --quiet -s 100 -b 1 -g test/genome/genome.fasta.gz -o SV/leviathanpop -p test/samples.groups 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet -g test/genome/genome.fasta.gz -o SV/naibr -x "-min_sv 5000" test/bam_phased && rm -r Genome | |
| - name: naibr pop | |
| if: always() | |
| shell: micromamba-shell {0} | |
| run: harpy sv naibr --quiet -g test/genome/genome.fasta.gz -o SV/pop -p test/samples.groups test/bam_phased && rm -r Genome | |
| - name: naibr with phasing | |
| if: always() | |
| shell: micromamba-shell {0} | |
| run: | | |
| harpy sv naibr --quiet -g test/genome/genome.fasta.gz -o SV/phase -v test/vcf/test.phased.bcf test/bam && rm -r Genome | |
| - name: naibr pop with phasing | |
| if: always() | |
| shell: micromamba-shell {0} | |
| run: harpy sv naibr --quiet -g test/genome/genome.fasta.gz -o SV/phasepop -v test/vcf/test.phased.bcf -p test/samples.groups 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet --snp-count 10 --indel-count 10 -z 0.5 test/genome/genome.fasta.gz | |
| harpy simulate snpindel --quiet --prefix Simulate/snpvcf --snp-vcf Simulate/snpindel/diploid/sim.snp.hap1.vcf --indel-vcf Simulate/snpindel/diploid/sim.indel.hap1.vcf test/genome/genome.fasta.gz | |
| - name: simulate inversions | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: | | |
| harpy simulate inversion --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz | |
| harpy simulate inversion --quiet --prefix Simulate/invvcf --vcf Simulate/inversion/diploid/sim.inversion.hap1.vcf test/genome/genome.fasta.gz | |
| - name: simulate cnv | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: | | |
| harpy simulate cnv --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz | |
| harpy simulate cnv --quiet --prefix Simulate/cnvvcf --vcf Simulate/cnv/diploid/sim.cnv.hap1.vcf test/genome/genome.fasta.gz | |
| - name: simulate translocations | |
| shell: micromamba-shell {0} | |
| if: always() | |
| run: | | |
| harpy simulate translocation --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz | |
| harpy simulate translocation --quiet --prefix Simulate/transvcf --vcf Simulate/translocation/diploid/sim.translocation.hap1.vcf 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 --quiet -t 4 -n 2 -l 100 -p 50 test/genome/genome.fasta.gz test/genome/genome2.fasta.gz | |
| assembly: | |
| needs: [changes, pkgbuild] | |
| if: ${{ needs.changes.outputs.assembly == 'true' && needs.pkgbuild.result == 'success' }} | |
| name: metassembly | |
| 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - name: Download Singularity Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: deps-image | |
| path: .snakemake/singularity | |
| - name: test assembly | |
| shell: micromamba-shell {0} | |
| run: harpy assembly --quiet -r 4000 test/fastq/sample1.* | |
| - name: test metassembly | |
| shell: micromamba-shell {0} | |
| run: harpy metassembly --quiet -r 4000 test/fastq/sample1.* | |
| - name: test metassembly without barcodes | |
| shell: micromamba-shell {0} | |
| run: harpy metassembly --ignore-bx --quiet -r 4000 test/fastq/sample1.* | |
| 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 | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 | |
| - name: harpy hpc | |
| shell: micromamba-shell {0} | |
| run: | | |
| harpy hpc slurm | |
| harpy hpc googlebatch | |
| harpy hpc lsf | |
| harpy hpc htcondor |