cwl/preprocess/cgivar/gvcf_regions.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: Extract called region from GVCF
   8 inputs:
   9   vcf:
  10     type: File
  11     label: Input GVCF
  12 outputs:
  13   bed:
  14     type: stdout
  15     label: BED region of GVCF
  16 baseCommand: /gvcf_regions/gvcf_regions.py
  17 arguments:
  18   - $(inputs.vcf)
  19   - "--unreported_is_called"
  20 stdout: $(inputs.vcf.nameroot).bed