WGS-processing/cwl/helper/bwa-gatk-report-wf.cwl

   1 cwlVersion: v1.1
   2 class: Workflow
   3
   4 requirements:
   5   - class: SubworkflowFeatureRequirement
   6
   7 inputs:
   8   fastq1: File
   9   fastq2: File
  10   reference:
  11     type: File
  12     secondaryFiles:
  13       - .amb
  14       - .ann
  15       - .bwt
  16       - .pac
  17       - .sa
  18       - .fai
  19       - ^.dict
  20   sample: string
  21   knownsites:
  22     type: File
  23     secondaryFiles:
  24       - .tbi
  25   scattercount: string
  26   clinvarvcf: File
  27   reportfunc: File
  28   headhtml: File
  29   tailhtml: File
  30
  31 outputs:
  32   qc-html:
  33     type: File[]
  34     outputSource: fastqc/out-html
  35   qc-zip:
  36     type: File[]
  37     outputSource: fastqc/out-zip
  38   gvcf:
  39     type: File
  40     outputSource: haplotypecaller/gatheredgvcf
  41   report:
  42     type: File
  43     outputSource: generate-report/report
  44 steps:
  45   fastqc:
  46     run: fastqc.cwl
  47     in:
  48       fastq1: fastq1
  49       fastq2: fastq2
  50     out: [out-html, out-zip]
  51   bwamem-samtools-view:
  52     run: bwamem-samtools-view.cwl
  53     in:
  54       fastq1: fastq1
  55       fastq2: fastq2
  56       reference: reference
  57       sample: sample
  58     out: [bam]
  59   samtools-sort:
  60     run: samtools-sort.cwl
  61     in:
  62       bam: bwamem-samtools-view/bam
  63       sample: sample
  64     out: [sortedbam]
  65   mark-duplicates:
  66     run: mark-duplicates.cwl
  67     in:
  68       bam: samtools-sort/sortedbam
  69     out: [dupbam,dupmetrics]
  70   samtools-index:
  71     run: samtools-index.cwl
  72     in:
  73       bam: mark-duplicates/dupbam
  74     out: [indexedbam]
  75   haplotypecaller:
  76     run: scatter-gatk-wf-with-interval.cwl
  77     in:
  78       reference: reference
  79       bam: samtools-index/indexedbam
  80       sample: sample
  81       scattercount: scattercount
  82       knownsites1: knownsites
  83     out: [gatheredgvcf]
  84   generate-report:
  85     run: report-wf.cwl
  86     in:
  87       gvcf: haplotypecaller/gatheredgvcf
  88       samplename: sample
  89       clinvarvcf: clinvarvcf
  90       reportfunc: reportfunc
  91       headhtml: headhtml
  92       tailhtml: tailhtml
  93     out: [report]