cwl/lightning/make-arrays.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 cwlVersion: v1.2
   6 class: ExpressionTool
   7 requirements:
   8   InlineJavascriptRequirement: {}
   9 inputs:
  10   matchgenome_array: string[]
  11   libdir_array: Directory[]
  12   genomeversion_array: string[]
  13   regions_nestedarray:
  14     type:
  15       type: array
  16       items:
  17         type: array
  18         items: [File, "null"]
  19   threads_array: int[]
  20   mergeoutput_array: string[]
  21   expandregions_array: int[]
  22 outputs:
  23   full_matchgenome_array: string[]
  24   full_libdir_array: Directory[]
  25   full_genomeversion_array: string[]
  26   full_regions_array:
  27     type:
  28       type: array
  29       items: [File, "null"]
  30   full_threads_array: int[]
  31   full_mergeoutput_array: string[]
  32   full_expandregions_array: int[]
  33   full_libname_array: string[]
  34 expression: |
  35   ${
  36     var full_matchgenome_array = [];
  37     var full_libdir_array = [];
  38     var full_genomeversion_array = [];
  39     var full_regions_array = [];
  40     var full_threads_array = [];
  41     var full_mergeoutput_array = [];
  42     var full_expandregions_array = [];
  43     var full_libname_array = [];
  44     for (var i = 0; i < inputs.matchgenome_array.length; i++) {
  45       for (var j = 0; j < inputs.libdir_array.length; j++) {
  46         for (var k = 0; k < inputs.regions_nestedarray[j].length; k++) {
  47           full_matchgenome_array.push(inputs.matchgenome_array[i]);
  48           full_libdir_array.push(inputs.libdir_array[j]);
  49           full_genomeversion_array.push(inputs.genomeversion_array[j]);
  50           full_regions_array.push(inputs.regions_nestedarray[j][k]);
  51           full_threads_array.push(inputs.threads_array[k]);
  52           full_mergeoutput_array.push(inputs.mergeoutput_array[k]);
  53           full_expandregions_array.push(inputs.expandregions_array[k]);
  54           var libname = inputs.genomeversion_array[j]+inputs.matchgenome_array[i]+"_library";
  55           full_libname_array.push(libname);
  56         }
  57       }
  58     }
  59     return {"full_matchgenome_array": full_matchgenome_array,
  60             "full_libdir_array": full_libdir_array, "full_genomeversion_array": full_genomeversion_array,
  61             "full_regions_array": full_regions_array, "full_threads_array": full_threads_array, "full_mergeoutput_array": full_mergeoutput_array, "full_expandregions_array": full_expandregions_array,
  62             "full_libname_array": full_libname_array};
  63   }