cwl/helper/gvcf-to-vcf.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Converts gvcf to vcf
   4
   5 requirements:
   6   - class: DockerRequirement
   7     dockerPull: curii/clinvar-report
   8   - class: ShellCommandRequirement
   9
  10 hints:
  11   ResourceRequirement:
  12     ramMin: 10000
  13     coresMin: 4
  14
  15 inputs:
  16   samplename:
  17     type: string
  18   gvcf:
  19     type: File
  20
  21 outputs:
  22   vcf:
  23     type: File
  24     outputBinding:
  25       glob: "*.vcf.gz"
  26     secondaryFiles: [.tbi]
  27
  28 arguments:
  29   - bcftools
  30   - view
  31   - prefix: "--min-ac"
  32     valueFrom: "1"
  33   - $(inputs.gvcf.path)
  34   - prefix: "-i"
  35     valueFrom: "AVG(GQ)>20"
  36   - valueFrom: "-Ov"
  37   - prefix: "-o"
  38     valueFrom: $(inputs.samplename).vcf
  39   - {valueFrom: '&&', shellQuote: false}
  40   - bgzip
  41   - valueFrom: $(inputs.samplename).vcf
  42   - {valueFrom: '&&', shellQuote: false}
  43   - tabix
  44   - valueFrom: $(inputs.samplename).vcf.gz