cwl/gvcf2fasta/scatter-gvcf2fasta_splitvcf-imputation-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: v1.1
   8 class: Workflow
   9 label: Scatter to impute gVCF and convert gVCF to FASTA
  10 requirements:
  11   SubworkflowFeatureRequirement: {}
  12   ScatterFeatureRequirement: {}
  13 hints:
  14   DockerRequirement:
  15     dockerPull: vcfutil
  16
  17 inputs:
  18   sampleids:
  19     type: string[]
  20     label: Sample IDs
  21   splitvcfdirs:
  22     type: Directory[]
  23     label: Input directory of split gVCFs
  24   gqcutoff:
  25     type: int
  26     label: GQ (Genotype Quality) cutoff for filtering
  27   genomebed:
  28     type: File
  29     label: Whole genome BED
  30   ref:
  31     type: File
  32     label: Reference FASTA
  33   chrs: string[]
  34   refsdir: Directory
  35   mapsdir: Directory
  36   panelnocallbed: File
  37   panelcallbed: File
  38
  39 outputs:
  40   fas:
  41     type:
  42       type: array
  43       items:
  44         type: array
  45         items: File
  46     label: Output pairs of FASTAs
  47     outputSource: gvcf2fasta_splitvcf-imputation-wf/fas
  48
  49 steps:
  50   gvcf2fasta_splitvcf-imputation-wf:
  51     run: gvcf2fasta_splitvcf-imputation-wf.cwl
  52     scatter: [sampleid, splitvcfdir]
  53     scatterMethod: dotproduct
  54     in:
  55       sampleid: sampleids
  56       splitvcfdir: splitvcfdirs
  57       gqcutoff: gqcutoff
  58       genomebed: genomebed
  59       ref: ref
  60       chrs: chrs
  61       refsdir: refsdir
  62       mapsdir: mapsdir
  63       panelnocallbed: panelnocallbed
  64       panelcallbed: panelcallbed
  65     out: [fas]