WGS-processing/cwl/helper/getfastq.cwl

   1 class: ExpressionTool
   2 cwlVersion: v1.1
   3 label: Find matching FASTQ pairs
   4 requirements:
   5   InlineJavascriptRequirement: {}
   6
   7 inputs:
   8   fastqdir:
   9     type: Directory
  10     label: Input directory of FASTQs
  11     loadListing: 'shallow_listing'
  12
  13 outputs:
  14   fastq1:
  15     type: File[]
  16     format: edam:format_1930 # FASTQ
  17     label: Half set of pair-end FASTQs (R1)
  18   fastq2:
  19     type: File[]
  20     format: edam:format_1930 # FASTQ
  21     label: Half set of pair-end FASTQs (R2)
  22   sample:
  23     type: string[]
  24     label: Sample Names
  25
  26 expression: |
  27   ${function compare(a, b) {
  28     var baseA = a.basename;
  29     var baseB = b.basename;
  30
  31     var comparison = 0;
  32     if (baseA > baseB) {
  33     comparison = 1;
  34     } else if (baseA < baseB) {
  35     comparison = -1;
  36     }
  37     return comparison;
  38     }
  39
  40     var fastq1 = [];
  41     var fastq2 = [];
  42     for (var i = 0; i < inputs.fastqdir.listing.length; i++) {
  43       var name = inputs.fastqdir.listing[i];
  44       name.format = 'http://edamontology.org/format_1930'
  45       if (name.basename.indexOf('_1.fastq.gz') != -1 ) {
  46         fastq1.push(name);
  47       }
  48       if (name.basename.indexOf('_2.fastq.gz') != -1 ) {
  49         fastq2.push(name);
  50       }
  51     }
  52
  53     fastq1 = fastq1.sort(compare)
  54     fastq2 = fastq2.sort(compare)
  55
  56     var sample = [];
  57
  58     for (var i = 0; i < fastq1.length; i++) {
  59       var name = fastq1[i].basename;
  60       var samplename = name.replace(/_1.fastq.gz/,'');
  61       sample.push(samplename);
  62       }
  63
  64
  65     return {"fastq1": fastq1, "fastq2": fastq2, "sample": sample};
  66   }
  67
  68
  69 s:codeRepository: https://github.com/arvados/arvados-tutorial
  70 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  71
  72 $namespaces:
  73  s: https://schema.org/
  74  edam: http://edamontology.org/
  75  arv: "http://arvados.org/cwl#"
  76  cwltool: "http://commonwl.org/cwltool#"
  77
  78 #$schemas:
  79 # - https://schema.org/version/latest/schema.rdf
  80 # - http://edamontology.org/EDAM_1.18.owl