WGS-processing/cwl/helper/getfastq.cwl

   1 $namespaces:
   2   arv: "http://arvados.org/cwl#"
   3   cwltool: "http://commonwl.org/cwltool#"
   4 class: ExpressionTool
   5 cwlVersion: v1.1
   6 label: Create array of gvcfs to process
   7 requirements:
   8   InlineJavascriptRequirement: {}
   9 inputs:
  10   fastjdir:
  11     type: Directory
  12     label: Input directory of fastj
  13     loadListing: 'shallow_listing'
  14 outputs:
  15   fastq1:
  16     type: File[]
  17   fastq2:
  18     type: File[]
  19 expression: |
  20   ${function compare(a, b) {
  21     var baseA = a.basename;
  22     var baseB = b.basename;
  23
  24     var comparison = 0;
  25     if (baseA > baseB) {
  26     comparison = 1;
  27     } else if (baseA < baseB) {
  28     comparison = -1;
  29     }
  30     return comparison;
  31     }
  32
  33     var fastq1 = [];
  34     var fastq2 = [];
  35     for (var i = 0; i < inputs.fastjdir.listing.length; i++) {
  36       var name = inputs.fastjdir.listing[i];
  37       if (name.basename.indexOf('_1.fastq.gz') != -1 ) {
  38         fastq1.push(name);
  39       }
  40       if (name.basename.indexOf('_2.fastq.gz') != -1 ) {
  41         fastq2.push(name);
  42       }
  43     }
  44
  45     fastq1 = fastq1.sort(compare)
  46     fastq2 = fastq2.sort(compare)
  47
  48     return {"fastq1": fastq1, "fastq2": fastq2};
  49   }