WGS-processing/cwl/wgs-processing-wf.cwl

   1 Version: v1.1
   2 class: Workflow
   3
   4 requirements:
   5   - class: SubworkflowFeatureRequirement
   6   - class: ScatterFeatureRequirement
   7
   8 inputs:
   9   fastqdir: Directory
  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   gvcf:
  33     type: File[]
  34     outputSource: bwamem-gatk-report/gvcf
  35   report:
  36     type: File[]
  37     outputSource: bwamem-gatk-report/report
  38
  39 steps:
  40   getfastq:
  41     run: ./helper/getfastq.cwl
  42     in:
  43       fastqdir: fastqdir
  44     out: [fastq1, fastq2]
  45
  46   bwamem-gatk-report:
  47     run: ./helper/bwamem-gatk-report-wf.cwl
  48     scatter: [fastq1, fastq2]
  49     scatterMethod: dotproduct
  50     in:
  51       fastq1: getfastq/fastq1
  52       fastq2: getfastq/fastq2
  53       reference: reference
  54       sample: sample
  55       knownsites: knownsites
  56       scattercount: scattercount
  57       clinvarvcf: clinvarvcf
  58       reportfunc: reportfunc
  59       headhtml: headhtml
  60       tailhtml: tailhtml
  61     out: [qc-html,qc-zip,gvcf,report]