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add SomaticSeq

Merged add SomaticSeq
BIOWDL-78 into develop
Merged Ruben Vorderman requested to merge BIOWDL-78 into develop

Created by: DavyCats

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  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 8eda5fed
    • somaticseq.wdl
    65 }
    66
    67 output {
    68 File indels = outputDir + if defined(classifierIndel)
    69 then "/SSeq.Classified.sINDEL.vcf"
    70 else "/Consensus.sINDEL.vcf"
    71 File snvs = outputDir + if defined(classifierSNV)
    72 then "/SSeq.Classified.sSNV.vcf"
    73 else "/Consensus.sSNV.vcf"
    74 File ensembleIndels = outputDir + "/Ensemble.sINDEL.tsv"
    75 File ensembleSNV = outputDir + "/Ensemble.sSNV.tsv"
    76 }
    77
    78 runtime {
    79 cpu: threads
    80 docker: "lethalfang/somaticseq:3.1.0"
    • Ruben Vorderman
      Ruben Vorderman @rhpvorderman ·
      Author Owner

      We want to hardcode the version here? For now this is ok. But we need to discuss this at some point in the biopet meeting.

      lethalfang? Is this the canonical owner of the somaticseq package?!

  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 8eda5fed
    • strelka.wdl
    85 86 }
    86 87
    87 88 command {
    89 set -e -o pipefail
    90 ~{preCommand}
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 8eda5fed
    • somaticseq.wdl
    65 }
    66
    67 output {
    68 File indels = outputDir + if defined(classifierIndel)
    69 then "/SSeq.Classified.sINDEL.vcf"
    70 else "/Consensus.sINDEL.vcf"
    71 File snvs = outputDir + if defined(classifierSNV)
    72 then "/SSeq.Classified.sSNV.vcf"
    73 else "/Consensus.sSNV.vcf"
    74 File ensembleIndels = outputDir + "/Ensemble.sINDEL.tsv"
    75 File ensembleSNV = outputDir + "/Ensemble.sSNV.tsv"
    76 }
    77
    78 runtime {
    79 cpu: threads
    80 docker: "lethalfang/somaticseq:3.1.0"
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