cwl/preprocess/cgivar/bedtools-intersect.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 cwlVersion: v1.0
   6 class: CommandLineTool
   7 label: Intersect VCF with BED
   8 requirements:
   9   ShellCommandRequirement: {}
  10 inputs:
  11   vcf:
  12     type: File
  13     label: Input VCF
  14   bed:
  15     type: File
  16     label: Input BED
  17 outputs:
  18   vcfgz:
  19     type: File
  20     label: Output VCF with records inside the BED region
  21     outputBinding:
  22       glob: "*.vcf.gz"
  23     secondaryFiles: [.tbi]
  24 baseCommand: [bedtools, intersect]
  25 arguments:
  26   - "-header"
  27   - prefix: "-a"
  28     valueFrom: $(inputs.vcf)
  29   - prefix: "-b"
  30     valueFrom: $(inputs.bed)
  31   - prefix: "-f"
  32     valueFrom: "1"
  33   - shellQuote: false
  34     valueFrom: "|"
  35   - "bgzip"
  36   - "-c"
  37   - shellQuote: false
  38     valueFrom: ">"
  39   - $(inputs.vcf.basename).gz
  40   - shellQuote: false
  41     valueFrom: "&&"
  42   - "tabix"
  43   - prefix: "-p"
  44     valueFrom: "vcf"
  45   - $(inputs.vcf.basename).gz