WGS-processing/cwl/helper/gather-vcf.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Gather GVCF using Picard
   4
   5 $namespaces:
   6   arv: "http://arvados.org/cwl#"
   7   cwltool: "http://commonwl.org/cwltool#"
   8
   9 requirements:
  10   DockerRequirement:
  11     dockerPull: broadinstitute/gatk:4.1.7.0
  12   ShellCommandRequirement: {}
  13   InlineJavascriptRequirement: {}
  14
  15 hints:
  16   ResourceRequirement:
  17     ramMin: 20000
  18     coresMin: 4
  19   arv:RuntimeConstraints:
  20     outputDirType: keep_output_dir
  21
  22 inputs:
  23   gvcfdir:
  24     type: Directory
  25     label: Input directory of GVCFs
  26     loadListing: 'shallow_listing'
  27   sample:
  28     type: string
  29     label: Sample Name
  30   reference:
  31     type: File
  32     format: edam:format_1929 # FASTA
  33     label: Reference genome
  34     secondaryFiles:
  35       - .amb
  36       - .ann
  37       - .bwt
  38       - .pac
  39       - .sa
  40       - .fai
  41       - ^.dict
  42 outputs:
  43   gatheredgvcf:
  44     type: File
  45     format: edam:format_3016 # GVCF
  46     label: Gathered GVCF
  47     secondaryFiles:
  48       - .tbi
  49     outputBinding:
  50       glob: "*.g.vcf.gz"
  51
  52 baseCommand: /gatk/gatk
  53
  54 arguments:
  55   - "--java-options"
  56   - "-Xmx8G"
  57   - MergeVcfs
  58   - shellQuote: false
  59     valueFrom: |
  60      ${function compare(a, b) {
  61       var baseA = a.basename;
  62       var baseB = b.basename;
  63
  64       var comparison = 0;
  65       if (baseA > baseB) {
  66       comparison = 1;
  67       } else if (baseA < baseB) {
  68       comparison = -1;
  69       }
  70       return comparison;
  71       }
  72
  73       var samples = [];
  74       for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
  75         var name = inputs.gvcfdir.listing[i];
  76         if (name.nameext ==='.gz' ) {
  77           samples.push(name.path);
  78         }
  79       }
  80       samples = samples.sort(compare);
  81       var sampleinput = [];
  82
  83       for (var i = 0; i < samples.length; i++) {
  84        var s1 = samples[i];
  85        sampleinput = sampleinput + "-I " + s1 + " "
  86       }
  87
  88       return sampleinput;
  89       }
  90   - prefix: "-O"
  91     valueFrom: $(inputs.sample).g.vcf.gz
  92
  93 s:codeRepository: https://github.com/arvados/arvados-tutorial
  94 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  95
  96 $namespaces:
  97  s: https://schema.org/
  98  edam: http://edamontology.org/
  99  arv: "http://arvados.org/cwl#"
 100  cwltool: "http://commonwl.org/cwltool#"
 101
 102 #$schemas:
 103 # - https://schema.org/version/latest/schema.rdf
 104 # - http://edamontology.org/EDAM_1.18.owl