cwl/preprocess/gvcf/filtercleangvcf.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: Filters gVCFs by a specified quality cutoff and cleans
  11 requirements:
  12   DockerRequirement:
  13     dockerPull: arvados/l7g
  14   ResourceRequirement:
  15     coresMin: 2
  16     ramMin: 8000
  17   ShellCommandRequirement: {}
  18 hints:
  19   arv:RuntimeConstraints:
  20     keep_cache: 4096
  21 inputs:
  22   gvcf:
  23     type: File
  24     label: Input gVCF file
  25     secondaryFiles: [.tbi]
  26   filtergvcf:
  27     type: File
  28     label: Code that filters gVCFs
  29     default:
  30       class: File
  31       location: src/filter-gvcf
  32   cutoff:
  33     type: int
  34     label: Filtering cutoff threshold
  35   keepgqdot:
  36     type: boolean?
  37     label: Flag for keeping GQ represented by "."
  38   cleanvcf:
  39     type: File
  40     label: Code that cleans gVCFs
  41     default:
  42       class: File
  43       location: src/cleanvcf.py
  44 outputs:
  45   filteredcleangvcf:
  46     type: File
  47     label: Filtered and clean gVCF
  48     outputBinding:
  49       glob: "*vcf.gz"
  50     secondaryFiles: [.tbi]
  51 baseCommand: zcat
  52 arguments:
  53   - $(inputs.gvcf)
  54   - shellQuote: false
  55     valueFrom: "|"
  56   - $(inputs.filtergvcf)
  57   - prefix: "-k"
  58     valueFrom: $(inputs.keepgqdot)
  59   - $(inputs.cutoff)
  60   - shellQuote: false
  61     valueFrom: "|"
  62   - $(inputs.cleanvcf)
  63   - shellQuote: false
  64     valueFrom: "|"
  65   - "bgzip"
  66   - "-c"
  67   - shellQuote: false
  68     valueFrom: ">"
  69   - $(inputs.gvcf.nameroot).gz
  70   - shellQuote: false
  71     valueFrom: "&&"
  72   - "tabix"
  73   - prefix: "-p"
  74     valueFrom: "vcf"
  75   - $(inputs.gvcf.nameroot).gz