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kf-workflows's Issues

workflow/tools versioning and organizing

Open this Issue to discuss how to better version and organize KF workflows in terms of tool versioning, docker images build and tags, CWL file names, workflow and tool ID and versions etc. And potentially how to automated the release process.

Initial idea is to create subrepo for each workflow, and link them back [this kf-workflows repo] (https://github.com/kids-first/kf-workflows/)

Currently on pre-cocleaning branch, we have something like this:

.
├── LICENSE
├── README.md
├── dockerfiles
│   ├── alpine-bwa-samtools
│   │   ├── 0.7.17
│   │   │   └── Dockerfile
│   │   └── latest
│   │       └── Dockerfile
│   ├── alpine-gatk
│   │   ├── 3.8
│   │   │   └── Dockerfile
│   │   └── latest
│   │       └── Dockerfile
│   └── alpine-picard
│       ├── 2.14.0
│       │   └── Dockerfile
│       └── latest
│           └── Dockerfile
├── tools
│   ├── bwa_mem_0.7.17.cwl
│   ├── bwa_mem_latest.cwl
│   ├── picard_markduplicates_2.14.0.cwl
│   ├── picard_markduplicates_latest.cwl
│   ├── picard_sortsam_2.14.0.cwl
│   └── picard_sortsam_latest.cwl
└── workflows
    ├── pre_cocleaning_workflow_1.0.cwl
    └── pre_cocleaning_workflow_latest.cwl

12 directories, 16 files

Alignment Workflow

Will document specific details as development occurs, but at a high level:

  • By read-group alignment by BWA-mem
  • Picard MarkDuplicates
  • GATK4 BQSR
  • Picard Metrics
  • Final output CRAM

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