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

   1 cwlVersion: v1.1
   2 class: Workflow
   3 label: Main WGS Processing Workflow
   4
   5 requirements:
   6   - class: SubworkflowFeatureRequirement
   7   - class: ScatterFeatureRequirement
   8
   9 inputs:
  10   fastqdir: Directory
  11   reference:
  12     type: File
  13     secondaryFiles:
  14       - .amb
  15       - .ann
  16       - .bwt
  17       - .pac
  18       - .sa
  19       - .fai
  20       - ^.dict
  21   sample: string
  22   knownsites:
  23     type: File
  24     secondaryFiles:
  25       - .tbi
  26   scattercount: string
  27   clinvarvcf: File
  28   reportfunc: File
  29   headhtml: File
  30   tailhtml: File
  31
  32 outputs:
  33   gvcf:
  34     type: File[]
  35     outputSource: bwamem-gatk-report/gvcf
  36   report:
  37     type: File[]
  38     outputSource: bwamem-gatk-report/report
  39
  40 steps:
  41   getfastq:
  42     run: ./helper/getfastq.cwl
  43     in:
  44       fastqdir: fastqdir
  45     out: [fastq1, fastq2, sample]
  46
  47   bwamem-gatk-report:
  48     run: ./helper/bwamem-gatk-report-wf.cwl
  49     scatter: [fastq1, fastq2, sample]
  50     scatterMethod: dotproduct
  51     in:
  52       fastq1: getfastq/fastq1
  53       fastq2: getfastq/fastq2
  54       reference: reference
  55       sample: getfastq/sample
  56       knownsites: knownsites
  57       scattercount: scattercount
  58       clinvarvcf: clinvarvcf
  59       reportfunc: reportfunc
  60       headhtml: headhtml
  61       tailhtml: tailhtml
  62     out: [qc-html,qc-zip,gvcf,report]
  63
  64 s:codeRepository: https://github.com/arvados/arvados-tutorial
  65 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  66
  67 $namespaces:
  68   s: https://schema.org/