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License: Apache License 2.0
Bioinformatics workflows for Kids First DRC
License: Apache License 2.0
Proposed: 30 trios (so 90 WGS) from each sequencing center to run.
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
Will document specific details as development occurs, but at a high level:
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