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   SoftwareRequirement:
  15     packages:
  16       BCFtools:
  17         specs: [ "https://identifiers.org/rrid/RRID:SCR_005227" ]
  18         version: [ "1.10.2" ]
  19
  20 stdout: $(inputs.vcf.nameroot).txt
  21
  22 inputs:
  23   vcf:
  24     type: File
  25     format: edam:format_3016 # VCF
  26     label: VCF extracted from GVCF
  27     secondaryFiles: [.tbi]
  28   clinvarvcf:
  29     type: File
  30     format: edam:format_3016 # VCF
  31     label: Reference VCF for ClinVar
  32
  33 outputs:
  34   reporttxt: stdout
  35   label: Annotated text from VCF
  36
  37 arguments:
  38   - bcftools
  39   - annotate
  40   - prefix: "-a"
  41     valueFrom: $(inputs.clinvarvcf.path)
  42   - prefix: "-c"
  43     valueFrom: "ID,INFO"
  44   - $(inputs.vcf.path)
  45   - {valueFrom: '|', shellQuote: false}
  46   - bcftools
  47   - filter
  48   - prefix: "-i"
  49     valueFrom: "INFO/ALLELEID>=1"
  50   - {valueFrom: '|', shellQuote: false}
  51   - bcftools
  52   - query
  53   - prefix: "-f"
  54     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"
  55
  56 $namespaces:
  57  s: https://schema.org/
  58  edam: http://edamontology.org/
  59
  60 #$schemas:
  61 # - https://schema.org/version/latest/schema.rdf
  62 # - http://edamontology.org/EDAM_1.18.owl