cwl/preprocess/portablevcf/bcftools-annotate.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: Remove unused annotations
   8 requirements:
   9   ShellCommandRequirement: {}
  10 hints:
  11   DockerRequirement:
  12     dockerPull: vcfutil
  13 inputs:
  14   vcfgz:
  15     type: File
  16     label: Input VCF
  17 outputs:
  18   annotatedvcfgz:
  19     type: File
  20     label: Annotated VCF
  21     outputBinding:
  22       glob: "*vcf.gz"
  23     secondaryFiles: [.tbi]
  24 baseCommand: [bcftools, annotate]
  25 arguments:
  26   - prefix: "-x"
  27     valueFrom: "INFO/customer_score1,INFO/customer_score2,INFO/ADP,INFO/ADP,INFO/HET,INFO/HOM,INFO/NC,INFO/WT,FORMAT/AO,FORMAT/GL,FORMAT/QA,FORMAT/SDP,FORMAT/RD,FORMAT/AD,FORMAT/FREQ,FORMAT/PVAL,FORMAT/RBQ,FORMAT/ABQ,FORMAT/RDF,FORMAT/RDR,FORMAT/ADF,FORMAT/ADR"
  28   - $(inputs.vcfgz)
  29   - prefix: "-O"
  30     valueFrom: "z"
  31   - prefix: "-o"
  32     valueFrom: $(inputs.vcfgz.basename)
  33   - shellQuote: False
  34     valueFrom: "&&"
  35   - "tabix"
  36   - prefix: "-p"
  37     valueFrom: "vcf"
  38   - $(inputs.vcfgz.basename)