cwl/preprocess/cgivar/scatter-cgivar2vcfbed-wf.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 cwlVersion: v1.0
   8 class: Workflow
   9 label: Scatter to convert CGIVARs to VCFs and BEDs
  10 requirements:
  11   SubworkflowFeatureRequirement: {}
  12   ScatterFeatureRequirement: {}
  13 hints:
  14   DockerRequirement:
  15     dockerPull: cgivar2vcfbed
  16 inputs:
  17   cgivarsdir:
  18     type: Directory
  19     label: Input directory of CGIVARs
  20   reference:
  21     type: File
  22     label: CRR reference used for cgatools
  23   cgascript:
  24     type: File
  25     label: Script invoking cgatools
  26     default:
  27       class: File
  28       location: cgatools-mkvcf.sh
  29   fixscript:
  30     type: File
  31     label: Script to fix VCF
  32     default:
  33       class: File
  34       location: fix_vcf.py
  35
  36 outputs:
  37   vcfgzs:
  38     type: File[]
  39     label: Output VCFs
  40     outputSource: cgivar2vcfbed-wf/vcfgz
  41   beds:
  42     type: File[]
  43     label: Output BEDs
  44     outputSource: cgivar2vcfbed-wf/bed
  45
  46 steps:
  47   getfiles:
  48     run: getfiles.cwl
  49     in:
  50       dir: cgivarsdir
  51     out: [cgivars, samples]
  52   cgivar2vcfbed-wf:
  53     run: cgivar2vcfbed-wf.cwl
  54     scatter: [cgivar, sample]
  55     scatterMethod: dotproduct
  56     in:
  57       cgivar: getfiles/cgivars
  58       sample: getfiles/samples
  59       reference: reference
  60       cgascript: cgascript
  61       fixscript: fixscript
  62     out: [vcfgz, bed]