{"id":28295822,"url":"https://github.com/populationgenomics/cpg-flow-gatk-sv","last_synced_at":"2026-03-05T21:05:04.901Z","repository":{"id":292965406,"uuid":"967844392","full_name":"populationgenomics/cpg-flow-gatk-sv","owner":"populationgenomics","description":"CPG-Flow implementation of the GATK-SV pipeline, deployed at the Centre for Population Genomics","archived":false,"fork":false,"pushed_at":"2026-01-27T23:26:34.000Z","size":198,"stargazers_count":0,"open_issues_count":4,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2026-01-28T12:31:29.260Z","etag":null,"topics":["bioinformatics","cpg","cpg-flow-pipeline","pipeline","workflow"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/populationgenomics.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-04-17T05:05:20.000Z","updated_at":"2026-01-27T23:26:38.000Z","dependencies_parsed_at":"2025-05-29T04:24:12.381Z","dependency_job_id":"7a36962c-904e-4bb3-9e30-b4c460686d57","html_url":"https://github.com/populationgenomics/cpg-flow-gatk-sv","commit_stats":null,"previous_names":["populationgenomics/cpg-flow-gatk-sv"],"tags_count":0,"template":false,"template_full_name":"populationgenomics/cpg-flow-pipeline-template","purl":"pkg:github/populationgenomics/cpg-flow-gatk-sv","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/populationgenomics%2Fcpg-flow-gatk-sv","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/populationgenomics%2Fcpg-flow-gatk-sv/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/populationgenomics%2Fcpg-flow-gatk-sv/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/populationgenomics%2Fcpg-flow-gatk-sv/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/populationgenomics","download_url":"https://codeload.github.com/populationgenomics/cpg-flow-gatk-sv/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/populationgenomics%2Fcpg-flow-gatk-sv/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30149951,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-05T16:58:46.102Z","status":"ssl_error","status_checked_at":"2026-03-05T16:58:45.706Z","response_time":93,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","cpg","cpg-flow-pipeline","pipeline","workflow"],"created_at":"2025-05-22T16:19:25.844Z","updated_at":"2026-03-05T21:05:04.868Z","avatar_url":"https://github.com/populationgenomics.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GATK-SV, in CPG-Flow\n\nCurrent Version: 0.1.26\n\nThis repository contains the GATK-SV workflow, which is a wrapper around the [GATK-SV Cromwell workflow](https://github.com/broadinstitute/gatk-sv). It has been migrated from [Production-Pipelines](https://github.com/populationgenomics/production-pipelines/tree/main/cpg_workflows/stages/gatk_sv). This has been generated as part of the migration from Production-Pipelines's CPG_workflows framework, to the separate CPG-Flow.\n\n## Workflows\n\nThis repository contains the following workflows:\n\n- `singlesample_workflow` - previously called `gatk_sv_singlesample`. This is the initial per-sample variant calling, generation of QC metrics following variant calling, through to batching of samples based on those metrics. The exact stages are:\n    1. [GatherSampleEvidence](https://github.com/broadinstitute/gatk-sv/blob/main/wdl/GatherSampleEvidence.wdl)\n    2. [EvidenceQC](https://github.com/broadinstitute/gatk-sv/blob/main/wdl/EvidenceQC.wdl)\n    3. `CreateSampleBatches` - a somewhat bespoke sample batching script\n\n- `multisample_workflow` - previously called `gatk_sv_multisample`. This is the Cohort based batch processing of clustered samples, through to a final joint-called dataset.\n\n## Structure\n\nFollowing a best-practices CPG-Flow structure, the repository is structured as follows:\n\n```commandline\n├── Dockerfile\n├── LICENSE\n├── README.md\n├── pull_request_template.md\n├── pyproject.toml\n└── src\n    ├── cpg_flow_gatk_sv\n    │   ├── __init__.py\n    │   ├── config_template.toml\n    │   ├── singlesample_workflow.py\n    │   ├── multisample_workflow.py\n    │   ├── jobs\n    │   │   ├── CreateSampleBatches.py\n    │   │   ├── EvidenceQC.py\n    │   │   ├── GatherSampleEvidence.py\n    │   │   └── ...\n    │   ├── scripts\n    │   │   ├── __init__.py\n    │   │   └── sample_batching.py\n    │   │   └── ...\n    │   └── utils.py\n```\n\nThis structure contains the following important files:\n\n- `pyproject.toml` - the build instructions and linter settings for the repository\n- `singlesample_workflow` - the Stages and workflow trigger for the first workflow\n- `multisample_workflow` - the Stages and workflow trigger for the second workflow\n- `jobs` - a directory containing the logic for each of the Stages in the workflow. Each file contains a single Stage, and is\n  named after the Stage it contains. This implements all the logic for a stage, including assembling the input dictionary to be passed to Cromwell.\n- `scripts` - a directory containing any scripts which are not part of the GATK-SV Cromwell workflow, but are used in the workflow. This includes any helper scripts, or CPG-custom logic.\n\n## Example invocation\n\nThis is designed to be run using analysis-runner, using a fully containerised installation of this codebase.\n\n```bash\nanalysis-runner \\\n    --skip-repo-checkout \\\n    --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-gatk-sv:0.1.26 \\\n    --dataset DATASET \\\n    --description 'GATK-SV, CPG-flow' \\\n    -o gatk-sv_cpg-flow \\\n    --access-level full \\\n    --config CONFIG \\\n    singlesample_workflow\n```\n\n## Development\n\nSemantic Versioning should be implemented with `bump-my-version`\n\n```commandline\nbump-my-version bump patch/minor/major\n```\n\nThis is using the configuration block inside `pyproject.toml`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpopulationgenomics%2Fcpg-flow-gatk-sv","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpopulationgenomics%2Fcpg-flow-gatk-sv","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpopulationgenomics%2Fcpg-flow-gatk-sv/lists"}