WGS-processing/cwl/helper/gather-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   gvcfdir:
  23     type: Directory
  24     label: Input directory of gvcfs
  25     loadListing: 'shallow_listing'
  26   sample: string
  27   reference:
  28     type: File
  29     secondaryFiles:
  30       - .amb
  31       - .ann
  32       - .bwt
  33       - .pac
  34       - .sa
  35       - .fai
  36       - ^.dict
  37 outputs:
  38   gatheredgvcf:
  39     type: File
  40     secondaryFiles:
  41       - .tbi
  42     outputBinding:
  43       glob: "*.g.vcf.gz"
  44
  45 baseCommand: /gatk/gatk
  46
  47 arguments:
  48   - "--java-options"
  49   - "-Xmx8G"
  50   - MergeVcfs
  51   - shellQuote: false
  52     valueFrom: |
  53      ${function compare(a, b) {
  54       var baseA = a.basename;
  55       var baseB = b.basename;
  56
  57       var comparison = 0;
  58       if (baseA > baseB) {
  59       comparison = 1;
  60       } else if (baseA < baseB) {
  61       comparison = -1;
  62       }
  63       return comparison;
  64       }
  65
  66       var samples = [];
  67       for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
  68         var name = inputs.gvcfdir.listing[i];
  69         if (name.nameext ==='.gz' ) {
  70           samples.push(name.path);
  71         }
  72       }
  73       samples = samples.sort(compare);
  74       var sampleinput = [];
  75
  76       for (var i = 0; i < samples.length; i++) {
  77        var s1 = samples[i];
  78        sampleinput = sampleinput + "-I " + s1 + " "
  79       }
  80
  81       return sampleinput;
  82       }
  83   - prefix: "-O"
  84     valueFrom: $(inputs.sample).g.vcf.gz