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   InitialWorkDirRequirement:
  13     listing:
  14       - $(inputs.gvcf1)
  15       - $(inputs.gvcf2)
  16
  17 hints:
  18   ResourceRequirement:
  19     ramMin: 20000
  20     coresMin: 4
  21   arv:RuntimeConstraints:
  22     outputDirType: keep_output_dir
  23
  24 inputs:
  25   gvcf1:
  26     type: File
  27   gvcf2:
  28     type: File
  29   sample: string
  30   reference:
  31     type: File
  32     secondaryFiles:
  33       - .amb
  34       - .ann
  35       - .bwt
  36       - .pac
  37       - .sa
  38       - .fai
  39       - ^.dict
  40 outputs:
  41   gatheredgvcf:
  42     type: File
  43     outputBinding:
  44       glob: "*g.vcf.gz"
  45
  46 baseCommand: /gatk/gatk
  47
  48 arguments:
  49   - "--java-options"
  50   - "-Xmx8G"
  51   - MergeVcfs
  52   - prefix: "-I"
  53     valueFrom: $(inputs.gvcf1.basename)
  54   - prefix: "-I"
  55     valueFrom: $(inputs.gvcf2.basename)
  56   - prefix: "-O"
  57     valueFrom: $(inputs.sample)g.vcf.gz