cwl/helper/gather-array-vcf.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Gathering vcf using Picard
   4 $namespaces:
   5   arv: "http://arvados.org/cwl#"
   6   cwltool: "http://commonwl.org/cwltool#"
   7
   8 requirements:
   9   DockerRequirement:
  10     dockerPull: broadinstitute/gatk:4.1.7.0
  11   ShellCommandRequirement: {}
  12   InlineJavascriptRequirement: {}
  13
  14 hints:
  15   ResourceRequirement:
  16     ramMin: 20000
  17     coresMin: 4
  18   arv:RuntimeConstraints:
  19     outputDirType: keep_output_dir
  20
  21 inputs:
  22   gvcfarray:
  23     type: File[]
  24   sample: string
  25   reference:
  26     type: File
  27     secondaryFiles:
  28       - .amb
  29       - .ann
  30       - .bwt
  31       - .pac
  32       - .sa
  33       - .fai
  34       - ^.dict
  35 outputs:
  36   gatheredgvcf:
  37     type: File
  38     secondaryFiles:
  39       - .tbi
  40     outputBinding:
  41       glob: "*.g.vcf.gz"
  42
  43 baseCommand: /gatk/gatk
  44
  45 arguments:
  46   - "--java-options"
  47   - "-Xmx8G"
  48   - MergeVcfs
  49   - shellQuote: false
  50     valueFrom: |
  51      ${function compare(a, b) {
  52       var baseA = a.basename;
  53       var baseB = b.basename;
  54
  55       var comparison = 0;
  56       if (baseA > baseB) {
  57       comparison = 1;
  58       } else if (baseA < baseB) {
  59       comparison = -1;
  60       }
  61       return comparison;
  62       }
  63
  64       var sortedarray = [];
  65       sortedarray = inputs.gvcfarray.sort(compare)
  66
  67       var samples = [];
  68       for (var i = 0; i < sortedarray.length; i++) {
  69         var name = sortedarray[i];
  70         if (name.nameext ==='.gz' ) {
  71           samples.push(name.path);
  72         }
  73       }
  74
  75       var sampleinput = "";
  76
  77       for (var i = 0; i < samples.length; i++) {
  78        var s1 = samples[i];
  79        sampleinput = sampleinput + "-I " + s1 + " "
  80       }
  81
  82       return sampleinput;
  83       }
  84   - prefix: "-O"
  85     valueFrom: $(inputs.sample).g.vcf.gz