cwl/preprocess/portablevcf/rtg-vcfeval.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: RTG vcfeval to compare VCFs
   8 hints:
   9   DockerRequirement:
  10     dockerPull: vcfutil
  11 inputs:
  12   baselinevcfgz:
  13     type: File
  14     label: Baseline VCF
  15     secondaryFiles: [.tbi]
  16   callsvcfgz:
  17     type: File
  18     label: Calls VCF
  19     secondaryFiles: [.tbi]
  20   sdf:
  21     type: Directory
  22     label: RTG reference directory
  23 outputs:
  24   summary:
  25     type: File
  26     label: Summary file
  27     outputBinding:
  28       glob: "eval/summary.txt"
  29 baseCommand: [rtg, vcfeval]
  30 arguments:
  31   - prefix: "-b"
  32     valueFrom: $(inputs.baselinevcfgz)
  33   - prefix: "-c"
  34     valueFrom: $(inputs.callsvcfgz)
  35   - prefix: "-t"
  36     valueFrom: $(inputs.sdf)
  37   - prefix: "-o"
  38     valueFrom: "eval"