cwl/gvcf2fasta/maingvcf2fasta.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 Convert various gVCF to FASTA
  10 requirements:
  11   SubworkflowFeatureRequirement: {}
  12   ScatterFeatureRequirement: {}
  13 hints:
  14   DockerRequirement:
  15     dockerPull: vcfutil
  16   arv:IntermediateOutput:
  17     outputTTL: 604800
  18
  19 inputs:
  20   vcfsinput:
  21     - type: record
  22       vcfsdir:
  23         type: Directory
  24         label: Input directory of VCFs
  25     - type: record
  26       vcfs:
  27         type: File[]
  28         label: Input VCFs in array of files
  29     - type: record
  30       vcftars:
  31         type: File[]
  32         label: Input VCF tars
  33   genomebed:
  34     type: File
  35     label: Whole genome BED
  36   ref:
  37     type: File
  38     label: Reference FASTA
  39
  40   gqcutoff:
  41     type: int?
  42     label: GQ (Genotype Quality) cutoff for filtering
  43   sampleids:
  44     type: string[]?
  45     label: Sample IDs
  46   chrs: string[]?
  47   refsdir: Directory?
  48   mapsdir: Directory?
  49   panelnocallbed: File?
  50   panelcallbed: File?
  51
  52
  53 outputs:
  54   fas:
  55     type:
  56       type: array
  57       items:
  58         type: array
  59         items: File
  60     label: Output pairs of FASTAs
  61     outputSource:
  62       - gvcf2fasta_nonrefvcf-wf/fas
  63       - gvcf2fasta_splitvcf-imputation-wf/fas
  64       - gvcf2fasta_splitvcf-wf/fas
  65       - gvcf2fasta_splitvcftar-wf/fas
  66       - gvcf2fasta-wf/fas
  67     pickValue: first_non_null
  68
  69 steps:
  70   gvcf2fasta_nonrefvcf-wf:
  71     run:  subworkflows/scatter/gvcf2fasta/gvcf2fasta_nonrefvcf-wf.cwl
  72     when: $(inputs.sampleid and inputs.vcfsinput.vcf)
  73     scatter: [sampleid, vcf]
  74     scatterMethod: dotproduct
  75     in:
  76       sampleid: sampleids
  77       vcf: vcfsinput
  78       gqcutoff: gqcutoff
  79       genomebed: genomebed
  80       ref: ref
  81     out: [fas]
  82
  83   gvcf2fasta_splitvcf-imputation-wf:
  84     run: subworkflows/scatter/gvcf2fasta/gvcf2fasta_splitvcf-imputation-wf.cwl
  85     when: $(inputs.sampleids and inputs.splitvcfdirs and inputs.chrs and inputs.refsdir and inputs.mapsdir and inputs.panelcallbed and inputs.panelnocallbed)
  86     scatter: [sampleid, splitvcfdir]
  87     scatterMethod: dotproduct
  88     in:
  89       sampleid: sampleids
  90       splitvcfdir: vcfsinput
  91       gqcutoff: gqcutoff
  92       genomebed: genomebed
  93       ref: ref
  94       chrs: chrs
  95       refsdir: refsdir
  96       mapsdir: mapsdir
  97       panelnocallbed: panelnocallbed
  98       panelcallbed: panelcallbed
  99     out: [fas]
 100
 101   gvcf2fasta_splitvcf-wf:
 102     run: subworkflows/scatter/gvcf2fasta/gvcf2fasta_splitvcf-wf.cwl
 103     when: $(inputs.sampleid and inputs.splitvcfdir)
 104     scatter: [sampleid, splitvcfdir]
 105     scatterMethod: dotproduct
 106     in:
 107       sampleid: sampleids
 108       splitvcfdir: vcfsinput
 109       gqcutoff: gqcutoff
 110       genomebed: genomebed
 111       ref: ref
 112     out: [fas]
 113   gvcf2fasta_splitvcftar-wf:
 114     run: subworkflows/scatter/gvcf2fasta/gvcf2fasta_splitvcftar-wf.cwl
 115     when: $(inputs.sampleids and inputs.vcftars)
 116     scatter: [sampleid, vcftar]
 117     scatterMethod: dotproduct
 118     in:
 119       sampleid: sampleids
 120       vcftar: vcfsinput
 121       gqcutoff: gqcutoff
 122       genomebed: genomebed
 123       ref: ref
 124     out: [fas]
 125   getfiles:
 126     run: subworkflows/scatter/helpers/getfiles.cwl
 127     in:
 128       dir: vcfsinput
 129     out: [vcfs, samples]
 130   gvcf2fasta-wf:
 131     run: subworkflows/scatter/gvcf2fasta/gvcf2fasta-wf.cwl
 132     scatter: [sampleid, vcf]
 133     scatterMethod: dotproduct
 134     in:
 135       sampleid: getfiles/samples
 136       vcf: getfiles/vcfs
 137       genomebed: genomebed
 138       ref: ref
 139     out: [fas]
 140