WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl

   1 cwlVersion: v1.1
   2 class: Workflow
   3 label: Scattered variant calling workflow
   4
   5 requirements:
   6   - class: SubworkflowFeatureRequirement
   7   - class: ScatterFeatureRequirement
   8
   9 inputs:
  10   bam:
  11     type: File
  12     format: edam:format_2572 # BAM
  13     label: Indexed sorted BAM with labeled duplicates
  14     secondaryFiles:
  15       - .bai
  16   reference:
  17     type: File
  18     format: edam:format_1929 # FASTA
  19     label: Reference genome
  20     secondaryFiles:
  21       - .amb
  22       - .ann
  23       - .bwt
  24       - .pac
  25       - .sa
  26       - .fai
  27       - ^.dict
  28   sample:
  29     type: string
  30     label: Sample Name
  31   knownsites1:
  32     type: File
  33     format: edam:format_3016 # VCF
  34     label: VCF of known polymorphic sites for BQSR
  35     secondaryFiles:
  36       - .tbi
  37   scattercount:
  38     type: string
  39     label: Desired split for variant calling
  40
  41 outputs:
  42   gatheredgvcf:
  43     type: File
  44     format: edam:format_3016 # GVCF
  45     label: Gathered GVCF
  46     secondaryFiles:
  47       - .tbi
  48     outputSource: gather-GVCFs/gatheredgvcf
  49
  50 steps:
  51   splitintervals:
  52     run: gatk-splitintervals.cwl
  53     in:
  54       reference: reference
  55       sample: sample
  56       scattercount: scattercount
  57     out: [intervalfiles]
  58
  59   recal-haplotypecaller:
  60     run: gatk-wf-with-interval.cwl
  61     scatter: intervallist
  62     in:
  63       bam: bam
  64       reference: reference
  65       sample: sample
  66       knownsites1: knownsites1
  67       intervallist: splitintervals/intervalfiles
  68     out: [gvcf]
  69
  70   gather-GVCFs:
  71     run: gather-array-vcf.cwl
  72     in:
  73       gvcfarray: recal-haplotypecaller/gvcf
  74       sample: sample
  75       reference: reference
  76     out: [gatheredgvcf]
  77
  78 s:codeRepository: https://github.com/arvados/arvados-tutorial
  79 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  80
  81 $namespaces:
  82  s: https://schema.org/
  83  edam: http://edamontology.org/
  84
  85 $schemas:
  86  - https://schema.org/version/latest/schema.rdf
  87  - http://edamontology.org/EDAM_1.18.owl