cwl/annotate-vcf.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3
   4 requirements:
   5   - class: DockerRequirement
   6     dockerPull: curii/clinvar-report
   7   - class: ShellCommandRequirement
   8
   9 hints:
  10   ResourceRequirement:
  11     ramMin: 10000
  12     coresMin: 4
  13
  14 stdout: $(inputs.vcf.nameroot).txt
  15
  16 arguments:
  17   - bcftools
  18   - annotate
  19   - prefix: "-a"
  20     valueFrom: $(inputs.clinvarvcf.path)
  21   - prefix: "-c"
  22     valueFrom: "ID,INFO"
  23   - $(inputs.vcf.path)
  24   - {valueFrom: '|', shellQuote: false}
  25   - bcftools
  26   - filter
  27   - prefix: "-i"
  28     valueFrom: "INFO/ALLELEID>=1"
  29
  30 inputs:
  31   vcf:
  32     type: File
  33   clinvarvcf:
  34     type: File
  35
  36 outputs:
  37   report: stdout