cwl/preprocess/simons/make-bed.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 $namespaces:
   6   arv: "http://arvados.org/cwl#"
   7 cwlVersion: v1.0
   8 class: CommandLineTool
   9 label: Make BED from VCF for regions passing a specified QUAL and GQ cutoff
  10 requirements:
  11   DockerRequirement:
  12     dockerPull: vcfutil
  13   ResourceRequirement:
  14     coresMin: 2
  15     ramMin: 22000
  16   ShellCommandRequirement: {}
  17 hints:
  18   arv:RuntimeConstraints:
  19     keep_cache: 4096
  20 inputs:
  21   vcf:
  22     type: File
  23     label: Input VCF file
  24   sample:
  25     type: string
  26     label: Sample name of VCF
  27   qualcutoff:
  28     type: int
  29     label: Filtering QUAL cutoff
  30   gqcutoff:
  31     type: int
  32     label: Filtering GQ cutoff
  33 outputs:
  34   bed:
  35     type: stdout
  36     label: BED for regions that pass cutoff
  37 baseCommand: [bcftools, view]
  38 arguments:
  39   - prefix: "-e"
  40     valueFrom: "QUAL<$(inputs.qualcutoff) | QUAL='.' | FORMAT/GQ<$(inputs.gqcutoff)"
  41   - $(inputs.vcf)
  42   - shellQuote: false
  43     valueFrom: "|"
  44   - "convert2bed"
  45   - prefix: "-i"
  46     valueFrom: "vcf"
  47   - "-d"
  48   - shellQuote: false
  49     valueFrom: "|"
  50   - "cut"
  51   - "-f1-3"
  52   - shellQuote: false
  53     valueFrom: "|"
  54   - "bedtools"
  55   - "merge"
  56   - prefix: "-i"
  57     valueFrom: "-"
  58 stdout: $(inputs.sample).bed