cwl/helper/gather-vcf-try2.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     outputBinding:
  41       glob: "*.g.vcf.gz"
  42
  43 baseCommand: /gatk/gatk
  44
  45 arguments:
  46   - "--java-options"
  47   - "-Xmx8G"
  48   - GatherVcfs
  49   - shellQuote: false
  50     valueFrom: >
  51     ${
  52     var samples = [];
  53     for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
  54       var name = inputs.gvcfdir.listing[i];
  55       if (name.nameext ==='.gz' ) {
  56         samples.push(name.basename);
  57       }
  58     }
  59     samples = samples.sort();
  60     var sampleinput = [];
  61
  62     for (var i = 0; i < samples.length; i++) {
  63      var s1 = samples[i];
  64      sampleinput = sampleinput + "-I " + s1 + " "
  65     }
  66     return sampleinput;
  67     }
  68   - prefix: "-O"
  69     valueFrom: $(inputs.sample).g.vcf.gz