dnanexus-rnd / deepvariant-glnexus-wdl Goto Github PK

Is it feasible to separate out htsget as a separate step/task? Whether or not it sits in a separate WDL isn't particularly critical, but I'm not sure how intrinsically linked the data access is with the DeepVariant call.

Relatedly, which of these parameters are specific to htsget?

{
    "DVGLx_test.accessions": ["NA12878","NA12891","NA12892"],
    "DVGLx_test.htsget_endpoint": "https://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_hg38",
    "DVGLx_test.htsget_format": "CRAM",
    "DVGLx_test.ranges": ["chr12:111766922-111817529","chr17:43045629-43125483"],
    "DVGLx_test.ref_fasta_gz": "dx://file-BFBv6J80634gkvZ6z100VGpp",
    "DVGLx_test.model_tar": "dx://file-FK3PKKQ04Py6V8Bj5YYpY60q",
    "DVGLx_test.deepvariant_docker": "quay.io/mlin/deepvariant:0.7.0",
    "DVGLx_test.output_name": "hg38_CEUtrio_ALDH2_BRCA1",
    "DVGLx_test.expected": "19chr12,186chr17,"
}

Brainstorming steps / tasks for Dockstore compatibility (and by extension, WES compatibility). Can iterate here as needed.

[ ] Conformance test / expected output
[ ] Checker workflow
[ ] Checker tool/task (optional)
[ ] Dockerized task(s) (optional)
[ ] Provide public inputs (e.g., not dx://)

@denis-yuen might have thoughts/suggestions as well.