cwl/imputation/rtg-vcffilter-bedtools-intersect.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 cwlVersion: v1.1
   6 class: CommandLineTool
   7 requirements:
   8   ShellCommandRequirement: {}
   9 hints:
  10   DockerRequirement:
  11     dockerPull: vcfutil
  12   ResourceRequirement:
  13     ramMin: 5000
  14 inputs:
  15   sample: string
  16   vcf:
  17     type: File
  18     secondaryFiles: [.tbi]
  19   bed: File
  20 outputs:
  21   filteredvcf:
  22     type: File
  23     outputBinding:
  24       glob: "*.vcf.gz"
  25     secondaryFiles: [.tbi]
  26 baseCommand: [rtg, vcffilter]
  27 arguments:
  28   - "--remove-overlapping"
  29   - prefix: "-i"
  30     valueFrom: $(inputs.vcf)
  31   - prefix: "-o"
  32     valueFrom: "-"
  33   - shellQuote: false
  34     valueFrom: "|"
  35   - "bedtools"
  36   - "intersect"
  37   - "-header"
  38   - prefix: "-f"
  39     valueFrom: "1"
  40   - prefix: "-a"
  41     valueFrom: "stdin"
  42   - prefix: "-b"
  43     valueFrom: $(inputs.bed)
  44   - shellQuote: false
  45     valueFrom: "|"
  46   - "bgzip"
  47   - "-c"
  48   - shellQuote: false
  49     valueFrom: ">"
  50   - $(inputs.sample).vcf.gz
  51   - shellQuote: false
  52     valueFrom: "&&"
  53   - "tabix"
  54   - $(inputs.sample).vcf.gz