cwl/helper/gather-vcf-try2.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Gathering vcf using Picard
   4 $namespaces:
   5   arv: "http://arvados.org/cwl#"
   6   cwltool: "http://commonwl.org/cwltool#"
   7
   8 requirements:
   9   DockerRequirement:
  10     dockerPull: broadinstitute/gatk:4.1.7.0
  11   ShellCommandRequirement: {}
  12   InlineJavascriptRequirement: {}
  13
  14 hints:
  15   ResourceRequirement:
  16     ramMin: 20000
  17     coresMin: 4
  18   arv:RuntimeConstraints:
  19     outputDirType: keep_output_dir
  20
  21 inputs:
  22   gvcfarray: File[]
  23   sample: string
  24   reference:
  25     type: File
  26     secondaryFiles:
  27       - .amb
  28       - .ann
  29       - .bwt
  30       - .pac
  31       - .sa
  32       - .fai
  33       - ^.dict
  34 outputs:
  35   gatheredgvcf:
  36     type: File
  37     outputBinding:
  38       glob: "*.g.vcf.gz"
  39
  40 baseCommand: /gatk/gatk
  41
  42 arguments:
  43   - "--java-options"
  44   - "-Xmx8G"
  45   - GatherVcfs
  46   - shellQuote: false
  47     valueFrom: >
  48       ${
  49         var cmd "";
  50         for( var i = 0; i < inputs.gvcfarray.length; i++){
  51            cmd += "\s echo " + "-I" + "\s" + inputs.gvcfsarray[i]
  52         }
  53         return cmd;
  54        }
  55   - prefix: "-O"
  56     valueFrom: $(inputs.sample).g.vcf.gz