cwl/helper/not-in-use/bwa-gatk-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
  22 outputs:
  23   qc-html:
  24     type: File[]
  25     outputSource: fastqc/out-html
  26   qc-zip:
  27     type: File[]
  28     outputSource: fastqc/out-zip
  29   vcf:
  30     type: File
  31     outputSource: haplotypecaller/vcf
  32
  33 steps:
  34   fastqc:
  35     run: fastqc.cwl
  36     in:
  37       fastq1: fastq1
  38       fastq2: fastq2
  39     out: [out-html, out-zip]
  40   bwamem-samtools-view:
  41     run: bwamem-samtools-view.cwl
  42     in:
  43       fastq1: fastq1
  44       fastq2: fastq2
  45       reference: reference
  46       sample: sample
  47     out: [bam]
  48   samtools-sort:
  49     run: samtools-sort.cwl
  50     in:
  51       bam: bwamem-samtools-view/bam
  52       sample: sample
  53     out: [out]
  54   samtools-index:
  55     run: samtools-index.cwl
  56     in:
  57       bam: samtools-sort/out
  58     out: [out]
  59   haplotypecaller:
  60     run: gatk-haplotypecaller.cwl
  61     in:
  62       reference: reference
  63       bam: samtools-index/out
  64       sample: sample
  65     out: [vcf]