Current Version: 0.1.24

This repository contains the GATK-SV workflow, which is a wrapper around the GATK-SV Cromwell workflow. It has been migrated from Production-Pipelines. This has been generated as part of the migration from Production-Pipelines's CPG_workflows framework, to the separate CPG-Flow.

This repository contains the following workflows:

• 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:

  1. GatherSampleEvidence
  2. EvidenceQC
  3. CreateSampleBatches - a somewhat bespoke sample batching script

• multisample_workflow - previously called gatk_sv_multisample. This is the Cohort based batch processing of clustered samples, through to a final joint-called dataset.

Following a best-practices CPG-Flow structure, the repository is structured as follows:

├── Dockerfile
├── LICENSE
├── README.md
├── pull_request_template.md
├── pyproject.toml
└── src
    ├── cpg_flow_gatk_sv
    │   ├── __init__.py
    │   ├── config_template.toml
    │   ├── singlesample_workflow.py
    │   ├── multisample_workflow.py
    │   ├── jobs
    │   │   ├── CreateSampleBatches.py
    │   │   ├── EvidenceQC.py
    │   │   ├── GatherSampleEvidence.py
    │   │   └── ...
    │   ├── scripts
    │   │   ├── __init__.py
    │   │   └── sample_batching.py
    │   │   └── ...
    │   └── utils.py

This structure contains the following important files:

• pyproject.toml - the build instructions and linter settings for the repository
• singlesample_workflow - the Stages and workflow trigger for the first workflow
• multisample_workflow - the Stages and workflow trigger for the second workflow
• jobs - a directory containing the logic for each of the Stages in the workflow. Each file contains a single Stage, and is named after the Stage it contains. This implements all the logic for a stage, including assembling the input dictionary to be passed to Cromwell.
• 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.

This is designed to be run using analysis-runner, using a fully containerised installation of this codebase.

analysis-runner \
    --skip-repo-checkout \
    --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-gatk-sv:0.1.24 \
    --dataset DATASET \
    --description 'GATK-SV, CPG-flow' \
    -o gatk-sv_cpg-flow \
    --access-level full \
    --config CONFIG \
    singlesample_workflow

Semantic Versioning should be implemented with bump-my-version

bump-my-version bump patch/minor/major

This is using the configuration block inside pyproject.toml