modules icon indicating copy to clipboard operation
modules copied to clipboard
verified publisher icon nf-core

Integration of Parabricks

Open famosab opened this issue 1 year ago • 0 comments

This is a list of parabricks modules that can be created during the Hackathon (just convert these into single issues when you start working on them).

Alignment

  • [x] fq2bam
  • [x] https://github.com/nf-core/modules/issues/6739
  • [ ] STAR
  • [x] #8626

Preprocessing

  • [x] applybqsr
  • [ ] bam2fq
  • [ ] bqsr
  • [ ] bamsort
  • [ ] markdup

Variant Calling

  • [x] haplotypecaller
  • [x] deepvariant
  • [x] mutectcaller
  • [ ] deepsomatic
  • [ ] starfusion

Quality Checks

  • [ ] bammetrics
  • [ ] collectmultiple metrics

GVCF Processing

  • [x] genotypegvcf
  • [x] indexgvcf
  • [x] dbsnp
  • [ ] prepon
  • [ ] postpon

famosab avatar Oct 15 '24 10:10 famosab