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

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