DNA-Seq pipeline Dev - germline variant calling workflow in nf-core framework

[edsu7]

Draft copy in: https://github.com/edsu7/nf-core-argogermline payload branch: https://github.com/icgc-argo-workflows/argo-modules/tree/germline_variant_payload

Once testing is done can be forked over to argo-workflows.

Testing commands:

• Full test

  nextflow run main.nf -profile test_full,docker,debug_qa --api_token <API_TOKEN> --local true

  Testing notes:

• There are three profiles along with docker,debug_qa
  • test_full - by default splits jobs by genome size for parallelism
  • test_no_intervals - disables job splitting
  • test_no_bed - If no bed is supplied uses genome.fasta.fai to generate bed
• Individual tools can be tested via specifying --tools
  • default value is : recalibrate,deepvariant,cnvkit,tiddit,manta,strelka,haplotypecaller
• Clean up of temporary files can be enabled by --cleanup
  • default value is : true
• Saving a local copy of variant calls (vcf.gz,vcf.gz.gzi) and payload json by specifying --local
  • default value is : true
  • setting false currently will result in an error as SCORE_UPLOAD will fail (see outstanding issues)

Currently outstanding issues:

• Schema for germline variant calls
• CNVKit to VCF calls
• Tiddit Supplement analysis package
• CNVKit Supplement analysis package
• Recalibration Supplement analysis package ?
• replace with ARGO readme.md

[edsu7]

Update variant_call and variant_call_supplement schemas to accept only normal analysisId

schema['properties']['workflow']['properties']['inputs']['minItems']=1

[edsu7]

clone over to icgc-argo-workflows

[edsu7]

PR to address issue Updated code to reflect separation of SNV and Indels

[edsu7]

Added a few more tools.

[edsu7]

Repo copied over to https://github.com/icgc-argo-workflows/germlinevar