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       if (name.basename.indexOf('_1.fastq.gz') != -1 ) {
  45         fastq1.push(name);
  46       }
  47       if (name.basename.indexOf('_2.fastq.gz') != -1 ) {
  48         fastq2.push(name);
  49       }
  50     }
  51
  52     fastq1 = fastq1.sort(compare)
  53     fastq2 = fastq2.sort(compare)
  54
  55     var sample = [];
  56
  57     for (var i = 0; i < fastq1.length; i++) {
  58       var name = fastq1[i].basename;
  59       var samplename = name.replace(/_1.fastq.gz/,'');
  60       sample.push(samplename);
  61       }
  62
  63
  64     return {"fastq1": fastq1, "fastq2": fastq2, "sample": sample};
  65   }
  66
  67
  68 s:codeRepository: https://github.com/arvados/arvados-tutorial
  69 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  70
  71 $namespaces:
  72  s: https://schema.org/
  73  edam: http://edamontology.org/
  74  arv: "http://arvados.org/cwl#"
  75  cwltool: "http://commonwl.org/cwltool#"
  76
  77 $schemas:
  78  - https://schema.org/version/latest/schema.rdf
  79  - http://edamontology.org/EDAM_1.18.owl