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| name: CI | ||
| on: | ||
| push: | ||
| pull_request: | ||
| schedule: | ||
| - cron: "0 0 1 * *" # run monthly | ||
| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| schedulers: ["gridengine", "slurm"] | ||
| env: | ||
| REGISTRY: ghcr.io | ||
| SCH: ${{ matrix.schedulers }} | ||
| IMAGE: ${{ github.repository_owner }}/sv-gen-${{ matrix.schedulers }} | ||
| TAG: "dev" | ||
| steps: | ||
| - name: Checkout repo | ||
| uses: actions/checkout@v2 | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v1 | ||
| with: | ||
| python-version: "3.9" | ||
| - name: Python info | ||
| run: | | ||
| which python | ||
| python --version | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install -r test-requirements.txt | ||
| - name: Show pip list | ||
| run: pip list | ||
| - name: Run unit tests | ||
| run: | | ||
| pytest --cov=helper_functions --cov-report=xml | ||
| mv coverage.xml ${{ github.workspace }} | ||
| working-directory: workflow | ||
| - name: Log into registry | ||
| uses: docker/login-action@v1 | ||
| with: | ||
| registry: ${{ env.REGISTRY }} | ||
| username: ${{ github.actor }} | ||
| password: ${{ secrets.GITHUB_TOKEN }} | ||
| - name: Run workflow | ||
| run: | | ||
| docker run -d -p 10000:22 --name $SCH ${REGISTRY}/${IMAGE,,}:${TAG} | ||
| sleep 10 | ||
| docker ps -a | ||
| docker exec -u xenon -t $SCH bash -c "cd sv-gen && ./run.sh $SCH" | ||
| - name: Upload coverage report to Codacy | ||
| uses: codacy/codacy-coverage-reporter-action@master | ||
| with: | ||
| project-token: ${{ secrets.CODACY_PROJECT_TOKEN }} | ||
| coverage-reports: coverage.xml |
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| usage: | ||
| software-stack-deployment: | ||
| conda: true | ||
| report: false |
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| { | ||
| "creators": [ | ||
| { | ||
| "affiliation": "Netherlands eScience Center", | ||
| "name": "Kuzniar, Arnold", | ||
| "orcid": "0000-0003-1711-7961" | ||
| }, | ||
| { | ||
| "affiliation": "University Medical Center Utrecht", | ||
| "name": "Santuari, Luca", | ||
| "orcid": "0000-0001-8784-2507" | ||
| } | ||
| ], | ||
| "keywords": [ | ||
| "bioinformatics", | ||
| "structural variants", | ||
| "cancer genomics", | ||
| "whole genome sequencing", | ||
| "workflow", | ||
| "simulation", | ||
| "high-performance computing", | ||
| "HPC", | ||
| "WGS", | ||
| "FASTA", | ||
| "BAM", | ||
| "VCF", | ||
| "BED" | ||
| ], | ||
| "license": { | ||
| "id": "Apache-2.0" | ||
| "creators": [ | ||
| { | ||
| "affiliation": "Netherlands eScience Center", | ||
| "name": "Kuzniar, Arnold", | ||
| "orcid": "0000-0003-1711-7961" | ||
| }, | ||
| "title": "sv-gen" | ||
| { | ||
| "affiliation": "University Medical Center Utrecht", | ||
| "name": "Santuari, Luca", | ||
| "orcid": "0000-0001-8784-2507" | ||
| } | ||
| ], | ||
| "keywords": [ | ||
| "bioinformatics", | ||
| "structural variants", | ||
| "cancer genomics", | ||
| "whole genome sequencing", | ||
| "workflow", | ||
| "simulation", | ||
| "high-performance computing", | ||
| "HPC", | ||
| "WGS", | ||
| "FASTA", | ||
| "BAM", | ||
| "VCF", | ||
| "BED" | ||
| ], | ||
| "license": { | ||
| "id": "Apache-2.0" | ||
| }, | ||
| "publication_date": "2023-01-18", | ||
| "title": "sv-gen", | ||
| "version": "1.1.0" | ||
| } |
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| ../README.md |
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| --- | ||
| threads: -1 # Samtools & BWA (default: -1 = set dynamically based on available cores) | ||
| memory: -1 # Samtools (default: -1 = set dynamically based on free memory per core [MB]) | ||
| tmpspace: 0 # Samtools (default: 0 [MB]) | ||
|
|
||
| # I/O files | ||
| input: | ||
| fasta: data/test.fasta # filepath of ref. genome (haploid) | ||
| seqids: [12, 22] # zero or more SeqIDs (e.g. chromosomes) | ||
|
|
||
| output: | ||
| basedir: data/out # relative or absolute path | ||
| genotype: # diploid genomes | ||
| - hmz # homozygous | ||
| - hmz-sv # homozygous with SVs | ||
| - htz-sv # heterozygous with SVs | ||
|
|
||
| # registered I/O file extensions | ||
| filext: | ||
| fasta: .fasta | ||
| fasta_idx: | ||
| - .fasta.ann # BWA v0.6.x index files | ||
| - .fasta.amb # | ||
| - .fasta.bwt # | ||
| - .fasta.pac # | ||
| - .fasta.sa # | ||
| fastq: .fq | ||
| bam: .bam | ||
| bam_idx: .bam.bai | ||
| bed: .bed | ||
| vcf: .vcf | ||
|
|
||
| simulation: | ||
| # SURVIVOR parameters | ||
| config: survivor.cfg | ||
| svtype: | ||
| dup: [0, 100, 10000] # duplication: [count, min_len, max_len] | ||
| inv: [0, 600, 800] # inversion: "" | ||
| tra: [10, 1000, 3000] # translocation: "" | ||
| indel: [10, 20, 500] # insertion+deletion: "" | ||
| invdel: [0, 600, 800] # inversion+deletion: "" | ||
| invdup: [0, 600, 800] # inversion+duplication: "" | ||
| # ART parameters | ||
| seed: 1000 | ||
| profile: HSXt | ||
| coverage: [10, 30] # [cov1, cov2, ...] | ||
| read: | ||
| length: [150] # [len1, len2, ...] | ||
| insert: | ||
| stdev: [10] # standard deviation of the fragment length (bp) | ||
| length: [500] # [len1, len2, ...] |
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