cwl/annotation/annotate-wf.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 cwlVersion: v1.1
   6 class: Workflow
   7 requirements:
   8   ScatterFeatureRequirement: {}
   9
  10 inputs:
  11   sample: string
  12   chrs: string[]
  13   vcfdir: Directory
  14   snpeffdatadir: Directory
  15   genomeversion: string
  16   dbsnp:
  17     type: File
  18     secondaryFiles: [.csi]
  19   gnomaddir: Directory
  20
  21 outputs:
  22   annotatedvcf:
  23     type: File
  24     secondaryFiles: [.tbi]
  25     outputSource: bcftools-concat/vcf
  26   summary:
  27     type: File
  28     outputSource: totalcounts/summary
  29
  30 steps:
  31   getfiles:
  32     run: getfiles.cwl
  33     in:
  34       sample: sample
  35       chrs: chrs
  36       vcfdir: vcfdir
  37       gnomaddir: gnomaddir
  38     out: [samples, vcfs, gnomads]
  39
  40   preprocess:
  41     run: preprocess.cwl
  42     scatter: [sample, vcf]
  43     scatterMethod: dotproduct
  44     in:
  45       sample: getfiles/samples
  46       vcf: getfiles/vcfs
  47     out: [trimmedvcf]
  48
  49   snpeff-bcftools-annotate:
  50     run: snpeff-bcftools-annotate.cwl
  51     scatter: [sample, vcf, gnomad]
  52     scatterMethod: dotproduct
  53     in:
  54       vcf: preprocess/trimmedvcf
  55       sample: getfiles/samples
  56       snpeffdatadir: snpeffdatadir
  57       genomeversion: genomeversion
  58       dbsnp: dbsnp
  59       gnomad: getfiles/gnomads
  60     out: [annotatedvcf]
  61
  62   bcftools-concat:
  63     run: bcftools-concat.cwl
  64     in:
  65       sample: sample
  66       vcfs: snpeff-bcftools-annotate/annotatedvcf
  67     out: [vcf]
  68
  69   getcount:
  70     run: getcount.cwl
  71     scatter: [sample, vcf]
  72     scatterMethod: dotproduct
  73     in:
  74       sample: getfiles/samples
  75       vcf: snpeff-bcftools-annotate/annotatedvcf
  76     out: [count]
  77
  78   totalcounts:
  79     run: totalcounts.cwl
  80     in:
  81       sample: sample
  82       counts: getcount/count
  83     out: [summary]