cypress/fixtures/workflow_with_array_fields.yaml

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 ---
   6 "$graph":
   7 - "$namespaces":
   8     arv: http://arvados.org/cwl#
   9   class: ExpressionTool
  10   doc: get the gct and vcf files, add other files
  11   expression: |
  12     $\{
  13       var fileArray = [];
  14
  15       // get files from collection
  16       for (var j = 0; j < inputs.collectionArray.length; j++) {
  17         for (var i = 0; i < inputs.collectionArray[j].listing.length; i++) {
  18           var matchedName = inputs.collectionArray[j].listing[i].basename.match(/^(.+)(.gct|.vcf|.vcf.gz|.gct.tsv|.vcf.tsv)$/);
  19           if (matchedName) {
  20             var nameString = inputs.collectionArray[j].listing[i].basename.split(".")[0]
  21             fileArray.push(inputs.collectionArray[j].listing[i])
  22           }
  23         }
  24       }
  25
  26       // get any other files from the input file array
  27       for (var i = 0; i < inputs.additionalFileArray.length; i++) {
  28         fileArray.push(inputs.additionalFileArray[i])
  29       }
  30
  31
  32       return {
  33         "collectedArray": fileArray,
  34         "nameString": nameString
  35       }
  36
  37     }
  38   id: "#collectFiles.cwl"
  39   inputs:
  40   - id: "#collectFiles.cwl/additionalFileArray"
  41     type:
  42       items: File
  43       type: array
  44   - id: "#collectFiles.cwl/collectionArray"
  45     type:
  46       items: Directory
  47       type: array
  48   outputs:
  49   - id: "#collectFiles.cwl/collectedArray"
  50     type:
  51       items: File
  52       type: array
  53   - id: "#collectFiles.cwl/nameString"
  54     type: string
  55   requirements:
  56   - class: InlineJavascriptRequirement
  57 - class: Workflow
  58   doc: A workflow to collect .gct and .vcf files files and store them together with
  59     specified metainformation files. Mostly used to create a collection for genestack
  60     upload. Can only be run on the WB2.
  61   hints:
  62   - class: ResourceRequirement
  63     coresMin: 1
  64     ramMin: 85000
  65   id: "#main"
  66   inputs:
  67   - default:
  68     - basename: metainfo.txt
  69       class: File
  70       location: keep:1cd1dbc27dc10fa8aaaf8fa19efd3bb8+237/metainfo.txt
  71       nameext: ".txt"
  72       nameroot: metainfo
  73       size: 0
  74     - basename: test11.txt
  75       class: File
  76       location: keep:1cd1dbc27dc10fa8aaaf8fa19efd3bb8+237/test11.txt
  77       nameext: ".txt"
  78       nameroot: test11
  79       size: 0
  80     doc: This input allows you to add any number of additional files to be integrated
  81       in the output collection.
  82     id: "#main/additionalFileArray"
  83     label: Files
  84     type:
  85       items: File
  86       type: array
  87   - default:
  88     - basename: collection1
  89       class: Directory
  90       location: keep:1cd1dbc27dc10fa8aaaf8fa19efd3bb8+237/collection1
  91     - basename: collection2
  92       class: Directory
  93       location: keep:1cd1dbc27dc10fa8aaaf8fa19efd3bb8+237/collection2
  94     doc: This input allows you to specify collections to integrate. From these collections,
  95       all files that end with .gct or .vcf will be extracted.
  96     id: "#main/collectionArray"
  97     label: Collections
  98     type:
  99       items: Directory
 100       type: array
 101   outputs:
 102   - id: "#main/genestackArray"
 103     outputSource: "#main/collectFiles/collectedArray"
 104     type:
 105       items: File
 106       type: array
 107   requirements:
 108   - class: SubworkflowFeatureRequirement
 109   - class: ScatterFeatureRequirement
 110   - class: StepInputExpressionRequirement
 111   - class: InlineJavascriptRequirement
 112   steps:
 113   - id: "#main/collectFiles"
 114     in:
 115     - id: "#main/collectFiles/additionalFileArray"
 116       source: "#main/additionalFileArray"
 117     - id: "#main/collectFiles/collectionArray"
 118       source: "#main/collectionArray"
 119     out:
 120     - "#main/collectFiles/collectedArray"
 121     run: "#collectFiles.cwl"
 122 cwlVersion: v1.0