WGS-processing/cwl/helper/annotate-vcf.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Annotate and filter 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 stdout: $(inputs.vcf.nameroot).txt
  16
  17 inputs:
  18   vcf:
  19     type: File
  20   clinvarvcf:
  21     type: File
  22
  23 outputs:
  24   reporttxt: stdout
  25
  26 arguments:
  27   - bcftools
  28   - annotate
  29   - prefix: "-a"
  30     valueFrom: $(inputs.clinvarvcf.path)
  31   - prefix: "-c"
  32     valueFrom: "ID,INFO"
  33   - $(inputs.vcf.path)
  34   - {valueFrom: '|', shellQuote: false}
  35   - bcftools
  36   - filter
  37   - prefix: "-i"
  38     valueFrom: "INFO/ALLELEID>=1"
  39   - {valueFrom: '|', shellQuote: false}
  40   - bcftools
  41   - query
  42   - prefix: "-f"
  43     valueFrom: "%ID\t%CHROM\t%POS\t%REF\t%ALT\t%INFO/ALLELEID\t%INFO/CLNSIG\t%INFO/CLNDN\t%INFO/AF_ESP\t%INFO/AF_EXAC\t%INFO/AF_TGP[\t%GT]\n"