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: v1.2
   8 class: Workflow
   9 label: Scatter to Convert various gVCF to FASTA
  10 requirements:
  11   SubworkflowFeatureRequirement: {}
  12   ScatterFeatureRequirement: {}
  13   MultipleInputFeatureRequirement: {}
  14   InlineJavascriptRequirement: {}
  15   StepInputExpressionRequirement: {}
  16 hints:
  17   DockerRequirement:
  18     dockerPull: vcfutil
  19   arv:IntermediateOutput:
  20     outputTTL: 604800
  21
  22 inputs:
  23   splitvcfdirs:
  24     type: Directory[]?
  25     label: Input directory of split gVCFs
  26     default: null
  27   vcfsdir:
  28     type: Directory?
  29     label: Input directory of VCFs
  30     default: null
  31   vcfs:
  32     type: File[]?
  33     label: Input VCFs in array of files
  34     default: null
  35   genomebed:
  36     type: File?
  37     label: Whole genome BED
  38     default: null
  39   ref:
  40     type: File?
  41     label: Reference FASTA
  42     default: null
  43   gqcutoff:
  44     type: int?
  45     label: GQ (Genotype Quality) cutoff for filtering
  46     default: null
  47   sampleids:
  48     type: string[]?
  49     label: Sample IDs
  50     default: null
  51   chrs: string[]?
  52   refsdir: Directory?
  53   mapsdir: Directory?
  54   panelnocallbed: File?
  55   panelcallbed: File?
  56   nonref: boolean?
  57   split: boolean?
  58   tar: boolean?
  59
  60
  61 outputs:
  62   fas:
  63     type:
  64       type: array
  65       items:
  66         type: array
  67         items: File
  68     label: Output pairs of FASTAs
  69     outputSource:
  70       - gvcf2fasta_nonrefvcf-wf/fas
  71       - gvcf2fasta_splitvcf-imputation-wf/fas
  72       - gvcf2fasta_splitvcf-wf/fas
  73       - gvcf2fasta_splitvcftar-wf/fas
  74       - gvcf2fasta-wf/fas
  75     pickValue: first_non_null
  76
  77 steps:
  78   getfiles:
  79     run: subworkflows/scatter/helpers/getfiles.cwl
  80     when: $(inputs.dir !== null)
  81     in:
  82       dir: vcfsdir
  83     out: [vcfs]
  84
  85   vcf_throttle:
  86     in:
  87       vcf_files:
  88         source: vcfs
  89         default: null
  90       transformed_vcfs:
  91         source: getfiles/vcfs
  92         default: null
  93     run: subworkflows/scatter/helpers/get_vcfs.cwl
  94     out: [vcfs]
  95
  96   get_sample_ids:
  97     run: subworkflows/scatter/helpers/get_sample_ids.cwl
  98     when: $(inputs.sampleids === null)
  99     in:
 100       vcfs: vcf_throttle/vcfs
 101       sampleids: sampleids
 102     out: [sampleids]
 103
 104   gvcf2fasta_nonrefvcf-wf:
 105     run:  subworkflows/scatter/gvcf2fasta/gvcf2fasta_nonrefvcf-wf.cwl
 106     when: $(inputs.vcf !== null && inputs.genomebed !== null && inputs.ref !== null && inputs.gqcutoff !== null && inputs.nonref === true)
 107     scatter: [sampleid, vcf]
 108     scatterMethod: dotproduct
 109     in:
 110       sampleid:
 111         source: get_sample_ids/sampleids
 112         default: []
 113       vcf:
 114         source: vcf_throttle/vcfs
 115         default: []
 116       gqcutoff: gqcutoff
 117       genomebed: genomebed
 118       ref: ref
 119       nonref: nonref
 120     out: [fas]
 121
 122   gvcf2fasta_splitvcf-imputation-wf:
 123     run: subworkflows/scatter/gvcf2fasta/gvcf2fasta_splitvcf-imputation-wf.cwl
 124     when: $(inputs.splitvcfdir !== null && inputs.chrs !== null && inputs.refsdir !== null && inputs.mapsdir !== null && inputs.panelcallbed !== null && inputs.panelnocallbed !== null)
 125     scatter: [sampleid, splitvcfdir]
 126     scatterMethod: dotproduct
 127     in:
 128       sampleid:
 129         source: sampleids
 130         default: []
 131       splitvcfdir:
 132         source: splitvcfdirs
 133         default: []
 134       gqcutoff: gqcutoff
 135       genomebed: genomebed
 136       ref: ref
 137       chrs: chrs
 138       refsdir: refsdir
 139       mapsdir: mapsdir
 140       panelnocallbed: panelnocallbed
 141       panelcallbed: panelcallbed
 142     out: [fas]
 143
 144   gvcf2fasta_splitvcf-wf:
 145     run: subworkflows/scatter/gvcf2fasta/gvcf2fasta_splitvcf-wf.cwl
 146     when: $(inputs.split && inputs.chrs === null)
 147     scatter: [sampleid, splitvcfdir]
 148     scatterMethod: dotproduct
 149     in:
 150       sampleid:
 151         source: get_sample_ids/sampleids
 152         default: []
 153       splitvcfdir:
 154         source: splitvcfdirs
 155         default: []
 156       gqcutoff: gqcutoff
 157       genomebed: genomebed
 158       ref: ref
 159       split: split
 160       chrs: chrs
 161     out: [fas]
 162
 163   gvcf2fasta_splitvcftar-wf:
 164     run: subworkflows/scatter/gvcf2fasta/gvcf2fasta_splitvcftar-wf.cwl
 165     when: $(inputs.tar === true && inputs.split === true)
 166     scatter: [sampleid, vcftar]
 167     scatterMethod: dotproduct
 168     in:
 169       sampleid:
 170         source: get_sample_ids/sampleids
 171         default: []
 172       vcftar:
 173         source: vcf_throttle/vcfs
 174         default: []
 175       gqcutoff: gqcutoff
 176       genomebed: genomebed
 177       ref: ref
 178       tar: tar
 179       split: split
 180     out: [fas]
 181   gvcf2fasta-wf:
 182     run: subworkflows/scatter/gvcf2fasta/gvcf2fasta-wf.cwl
 183     scatter: [sampleid, vcf]
 184     when: $(inputs.tar !== true && inputs.split !== true && inputs.nonref !== true)
 185     scatterMethod: dotproduct
 186     in:
 187       sampleid:
 188         source: get_sample_ids/sampleids
 189         default: []
 190       vcf:
 191         source: vcf_throttle/vcfs
 192         default: []
 193       genomebed: genomebed
 194       ref: ref
 195       gqcutoff: gqcutoff
 196       tar: tar
 197       split: split
 198       nonref: nonref
 199     out: [fas]
 200