cwl/preprocess/gvcf/getfiles.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 $namespaces:
   6   cwltool: "http://commonwl.org/cwltool#"
   7 class: ExpressionTool
   8 label: Create list of gVCFs from directory
   9 cwlVersion: v1.0
  10 requirements:
  11   InlineJavascriptRequirement: {}
  12 hints:
  13   cwltool:LoadListingRequirement:
  14     loadListing: shallow_listing
  15 inputs:
  16   gvcfdir:
  17     type: Directory
  18     label: Directory of input gVCFs
  19 outputs:
  20   gvcfs:
  21     type: File[]
  22     label: Array of gvcfs
  23     secondaryFiles: [.tbi]
  24 expression: |
  25   ${
  26     var gvcfs = [];
  27     for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
  28       var file = inputs.gvcfdir.listing[i];
  29       if (file.nameext == '.gz') {
  30         var main = file;
  31         for (var j = 0; j < inputs.gvcfdir.listing.length; j++) {
  32           var file = inputs.gvcfdir.listing[j];
  33           if (file.basename == main.basename+".tbi") {
  34             main.secondaryFiles = [file];
  35           }
  36         }
  37         gvcfs.push(main);
  38       }
  39     }
  40     return {"gvcfs": gvcfs};
  41   }