cwl/preprocess/chrmvcf/fixchrm.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   cwltool: "http://commonwl.org/cwltool#"
   8 cwlVersion: v1.0
   9 class: CommandLineTool
  10 label: Fix VCF by processing chrM
  11 requirements:
  12   DockerRequirement:
  13     dockerPull: vcfutil
  14   ResourceRequirement:
  15     coresMin: 2
  16     ramMin: 8000
  17 hints:
  18   arv:RuntimeConstraints:
  19     keep_cache: 4096
  20 inputs:
  21   vcf:
  22     type: File
  23     label: Input VCF file
  24   filterjs:
  25     type: File
  26     label: Javascript code for filtering
  27 outputs:
  28   fixedvcf:
  29     type: File
  30     label: Fixed VCF
  31     outputBinding:
  32       glob: "*vcf.gz"
  33     secondaryFiles: [.tbi]
  34 baseCommand: [rtg, vcffilter]
  35 arguments:
  36   - prefix: "-i"
  37     valueFrom: $(inputs.vcf)
  38   - prefix: "-o"
  39     valueFrom: $(inputs.vcf.basename)
  40   - prefix: "--javascript"
  41     valueFrom: $(inputs.filterjs)