cwl/lightning/stage-output.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 hints:
  10   LoadListingRequirement:
  11     loadListing: shallow_listing
  12 inputs:
  13   libname: string
  14   npyfiles: File[]
  15   onehotnpyfiles: File[]
  16   pcapngs: File[]
  17   bed: File
  18   annotatedvcf: File
  19   summary: File
  20 outputs:
  21   stagednpydir: Directory
  22   stagedonehotnpydir: Directory
  23   stagedannotationdir: Directory
  24 expression: |
  25   ${
  26     var stagednpydir = {"class": "Directory",
  27                         "basename": "library_full",
  28                         "listing": inputs.npyfiles};
  29     var stagedonehotnpydir = {"class": "Directory",
  30                               "basename": "library_filtered",
  31                               "listing": inputs.onehotnpyfiles};
  32     var annotationlist = inputs.pcapngs;
  33     annotationlist.push(inputs.bed);
  34     annotationlist.push(inputs.annotatedvcf);
  35     annotationlist.push(inputs.summary);
  36     var stagedannotationdir = {"class": "Directory",
  37                                 "basename": inputs.libname+"_annotation",
  38                                 "listing": annotationlist};
  39     return {"stagednpydir": stagednpydir, "stagedonehotnpydir": stagedonehotnpydir, "stagedannotationdir": stagedannotationdir};
  40   }