cwl/bwa-gatk-wf.cwl

   1 cwlVersion: v1.1
   2 class: Workflow
   3
   4 inputs:
   5   fastq1: File
   6   fastq2: File
   7   reference:
   8     type: File
   9     secondaryFiles:
  10       - .amb
  11       - .ann
  12       - .bwt
  13       - .pac
  14       - .sa
  15       - .fai
  16       - ^.dict
  17   sample: string
  18
  19 outputs:
  20   qc-html:
  21     type: File[]
  22     outputSource: fastqc/out-html
  23   qc-zip:
  24     type: File[]
  25     outputSource: fastqc/out-zip
  26   vcf:
  27     type: File
  28     outputSource: vep/out-vcf
  29
  30 steps:
  31   fastqc:
  32     run: fastqc.cwl
  33     in:
  34       fastq1: fastq1
  35       fastq2: fastq2
  36     out: [out-html, out-zip]
  37   bwamem-samtools-view:
  38     run: bwamem-samtools-view.cwl
  39     in:
  40       fastq1: fastq1
  41       fastq2: fastq2
  42       reference: reference
  43       sample: sample
  44     out: [bam]
  45   samtools-sort:
  46     run: samtools-sort.cwl
  47     in:
  48       bam: bwamem-samtools-view/bam
  49       sample: sample
  50     out: [out]
  51   samtools-index:
  52     run: samtools-index.cwl
  53     in:
  54       bam: samtools-sort/out
  55     out: [out]
  56   haplotypecaller:
  57     run: gatk-haplotypecaller.cwl
  58     in:
  59       reference: reference
  60       bam: samtools-index/out
  61       sample: sample
  62     out: [vcf]