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annotate planemo/lib/python3.7/site-packages/cwltool/schemas/v1.0/Workflow.yml @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 $base: "https://w3id.org/cwl/cwl#"
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2
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3 $namespaces:
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4 cwl: "https://w3id.org/cwl/cwl#"
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5 rdfs: "http://www.w3.org/2000/01/rdf-schema#"
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6
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7 $graph:
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8
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9 - name: "WorkflowDoc"
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10 type: documentation
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11 doc:
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12 - |
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13 # Common Workflow Language (CWL) Workflow Description, v1.0.2
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14
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15 This version:
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16 * https://w3id.org/cwl/v1.0/
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17
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18 Current version:
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19 * https://w3id.org/cwl/
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20 - "\n\n"
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21 - {$include: contrib.md}
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22 - "\n\n"
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23 - |
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24 # Abstract
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25
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26 One way to define a workflow is: an analysis task represented by a
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27 directed graph describing a sequence of operations that transform an
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28 input data set to output. This specification defines the Common Workflow
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29 Language (CWL) Workflow description, a vendor-neutral standard for
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30 representing workflows intended to be portable across a variety of
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31 computing platforms.
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32
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33 - {$include: intro.md}
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34
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35 - |
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36
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37 ## Introduction to CWL Workflow standard v1.0.2
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38
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39 This specification represents the third stable release from the CWL
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40 group. Since the initial v1.0 release, v1.0.2 introduces the following
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41 updates to the CWL Command Line Tool standard. Documents should continue
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42 to use `cwlVersion: v1.0` and existing v1.0 documents remain valid,
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43 however CWL documents that relied on previously undefined or
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44 underspecified behavior may have slightly different behavior in v1.0.2.
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45
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46 * 12 March 2017:
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47 * Mark `default` as not required for link checking.
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48 * Add note that recursive subworkflows is not allowed.
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49 * Fix mistake in discussion of extracting field names from workflow step ids.
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50 * 23 July 2017: (v1.0.1)
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51 * Add clarification about scattering over empty arrays.
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52 * Clarify interpretation of `secondaryFiles` on inputs.
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53 * Expanded discussion of semantics of `File` and `Directory` types
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54 * Fixed typo "EMACScript" to "ECMAScript"
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55 * Clarified application of input parameter default values when the input is `null` or undefined.
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56 * 10 August 2017: (v1.0.2)
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57 * Clarify behavior resolving expressions in `secondaryFile`
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58
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59 Since draft-3, v1.0 introduces the following changes and additions
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60 to the CWL Workflow standard:
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61
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62 * The `inputs` and `outputs` fields have been renamed `in` and `out`.
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63 * Syntax simplifcations: denoted by the `map<>` syntax. Example: `in`
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64 contains a list of items, each with an id. Now one can specify
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65 a mapping of that identifier to the corresponding
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66 `InputParameter`.
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67 ```
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68 in:
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69 - id: one
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70 type: string
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71 doc: First input parameter
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72 - id: two
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73 type: int
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74 doc: Second input parameter
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75 ```
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76 can be
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77 ```
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78 in:
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79 one:
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80 type: string
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81 doc: First input parameter
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82 two:
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83 type: int
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84 doc: Second input parameter
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85 ```
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86 * The common field `description` has been renamed to `doc`.
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87
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88 ## Purpose
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89
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90 The Common Workflow Language Command Line Tool Description express
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91 workflows for data-intensive science, such as Bioinformatics, Chemistry,
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92 Physics, and Astronomy. This specification is intended to define a data
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93 and execution model for Workflows that can be implemented on top of a
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94 variety of computing platforms, ranging from an individual workstation to
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95 cluster, grid, cloud, and high performance computing systems.
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96
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97 - {$include: concepts.md}
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98
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99 - name: ExpressionToolOutputParameter
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100 type: record
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101 extends: OutputParameter
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102 fields:
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103 - name: type
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104 type:
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105 - "null"
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106 - "#CWLType"
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107 - "#OutputRecordSchema"
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108 - "#OutputEnumSchema"
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109 - "#OutputArraySchema"
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110 - string
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111 - type: array
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112 items:
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113 - "#CWLType"
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114 - "#OutputRecordSchema"
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115 - "#OutputEnumSchema"
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116 - "#OutputArraySchema"
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117 - string
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118 jsonldPredicate:
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119 "_id": "sld:type"
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120 "_type": "@vocab"
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121 refScope: 2
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122 typeDSL: True
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123 doc: |
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124 Specify valid types of data that may be assigned to this parameter.
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125
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126 - type: record
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127 name: ExpressionTool
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128 extends: Process
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129 specialize:
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130 - specializeFrom: "#OutputParameter"
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131 specializeTo: "#ExpressionToolOutputParameter"
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132 documentRoot: true
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133 doc: |
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134 Execute an expression as a Workflow step.
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135 fields:
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136 - name: "class"
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137 jsonldPredicate:
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138 "_id": "@type"
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139 "_type": "@vocab"
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140 type: string
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141 - name: expression
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142 type: [string, Expression]
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143 doc: |
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144 The expression to execute. The expression must return a JSON object which
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145 matches the output parameters of the ExpressionTool.
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146
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147 - name: LinkMergeMethod
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148 type: enum
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149 docParent: "#WorkflowStepInput"
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150 doc: The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput).
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151 symbols:
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152 - merge_nested
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153 - merge_flattened
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154
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155
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156 - name: WorkflowOutputParameter
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157 type: record
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158 extends: OutputParameter
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159 docParent: "#Workflow"
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160 doc: |
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161 Describe an output parameter of a workflow. The parameter must be
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162 connected to one or more parameters defined in the workflow that will
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163 provide the value of the output parameter.
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164 fields:
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165 - name: outputSource
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166 doc: |
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167 Specifies one or more workflow parameters that supply the value of to
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168 the output parameter.
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169 jsonldPredicate:
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170 "_id": "cwl:outputSource"
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171 "_type": "@id"
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172 refScope: 0
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173 type:
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174 - string?
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175 - string[]?
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176 - name: linkMerge
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177 type: ["null", "#LinkMergeMethod"]
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178 jsonldPredicate: "cwl:linkMerge"
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179 doc: |
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180 The method to use to merge multiple sources into a single array.
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181 If not specified, the default method is "merge_nested".
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182 - name: type
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183 type:
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184 - "null"
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185 - "#CWLType"
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186 - "#OutputRecordSchema"
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187 - "#OutputEnumSchema"
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188 - "#OutputArraySchema"
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189 - string
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190 - type: array
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191 items:
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192 - "#CWLType"
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193 - "#OutputRecordSchema"
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194 - "#OutputEnumSchema"
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195 - "#OutputArraySchema"
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196 - string
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197 jsonldPredicate:
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198 "_id": "sld:type"
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199 "_type": "@vocab"
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200 refScope: 2
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201 typeDSL: True
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202 doc: |
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203 Specify valid types of data that may be assigned to this parameter.
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204
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205
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206 - name: Sink
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207 type: record
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208 abstract: true
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209 fields:
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210 - name: source
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211 doc: |
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212 Specifies one or more workflow parameters that will provide input to
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213 the underlying step parameter.
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214 jsonldPredicate:
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215 "_id": "cwl:source"
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216 "_type": "@id"
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217 refScope: 2
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218 type:
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219 - string?
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220 - string[]?
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221 - name: linkMerge
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222 type: LinkMergeMethod?
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223 jsonldPredicate: "cwl:linkMerge"
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224 doc: |
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225 The method to use to merge multiple inbound links into a single array.
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226 If not specified, the default method is "merge_nested".
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227
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228
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229 - type: record
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230 name: WorkflowStepInput
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231 extends: Sink
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232 docParent: "#WorkflowStep"
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233 doc: |
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234 The input of a workflow step connects an upstream parameter (from the
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235 workflow inputs, or the outputs of other workflows steps) with the input
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236 parameters of the underlying step.
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237
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238 ## Input object
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239
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240 A WorkflowStepInput object must contain an `id` field in the form
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241 `#fieldname` or `#prefix/fieldname`. When the `id` field contains a slash
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242 `/` the field name consists of the characters following the final slash
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243 (the prefix portion may contain one or more slashes to indicate scope).
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244 This defines a field of the workflow step input object with the value of
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245 the `source` parameter(s).
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246
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247 ## Merging
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248
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249 To merge multiple inbound data links,
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250 [MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified
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251 in the workflow or workflow step requirements.
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252
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253 If the sink parameter is an array, or named in a [workflow
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254 scatter](#WorkflowStep) operation, there may be multiple inbound data links
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255 listed in the `source` field. The values from the input links are merged
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256 depending on the method specified in the `linkMerge` field. If not
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257 specified, the default method is "merge_nested".
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258
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259 * **merge_nested**
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260
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261 The input must be an array consisting of exactly one entry for each
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262 input link. If "merge_nested" is specified with a single link, the value
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263 from the link must be wrapped in a single-item list.
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264
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265 * **merge_flattened**
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266
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267 1. The source and sink parameters must be compatible types, or the source
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268 type must be compatible with single element from the "items" type of
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269 the destination array parameter.
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270 2. Source parameters which are arrays are concatenated.
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271 Source parameters which are single element types are appended as
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272 single elements.
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273
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274 fields:
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275 - name: id
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276 type: string
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277 jsonldPredicate: "@id"
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278 doc: "A unique identifier for this workflow input parameter."
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279 - name: default
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280 type: ["null", Any]
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281 doc: |
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282 The default value for this parameter to use if either there is no
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283 `source` field, or the value produced by the `source` is `null`. The
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284 default must be applied prior to scattering or evaluating `valueFrom`.
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285 jsonldPredicate:
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286 _id: "cwl:default"
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287 noLinkCheck: true
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288 - name: valueFrom
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289 type:
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290 - "null"
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291 - "string"
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292 - "#Expression"
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293 jsonldPredicate: "cwl:valueFrom"
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294 doc: |
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295 To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must
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296 be specified in the workflow or workflow step requirements.
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297
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298 If `valueFrom` is a constant string value, use this as the value for
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299 this input parameter.
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300
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301 If `valueFrom` is a parameter reference or expression, it must be
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302 evaluated to yield the actual value to be assiged to the input field.
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303
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304 The `self` value of in the parameter reference or expression must be
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305 the value of the parameter(s) specified in the `source` field, or
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306 null if there is no `source` field.
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307
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308 The value of `inputs` in the parameter reference or expression must be
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309 the input object to the workflow step after assigning the `source`
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310 values, applying `default`, and then scattering. The order of
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311 evaluating `valueFrom` among step input parameters is undefined and the
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312 result of evaluating `valueFrom` on a parameter must not be visible to
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313 evaluation of `valueFrom` on other parameters.
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314
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315
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316 - type: record
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317 name: WorkflowStepOutput
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318 docParent: "#WorkflowStep"
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319 doc: |
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320 Associate an output parameter of the underlying process with a workflow
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321 parameter. The workflow parameter (given in the `id` field) be may be used
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322 as a `source` to connect with input parameters of other workflow steps, or
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323 with an output parameter of the process.
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324 fields:
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325 - name: id
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326 type: string
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327 jsonldPredicate: "@id"
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328 doc: |
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329 A unique identifier for this workflow output parameter. This is the
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330 identifier to use in the `source` field of `WorkflowStepInput` to
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331 connect the output value to downstream parameters.
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332
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333
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334 - name: ScatterMethod
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335 type: enum
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336 docParent: "#WorkflowStep"
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337 doc: The scatter method, as described in [workflow step scatter](#WorkflowStep).
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338 symbols:
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339 - dotproduct
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340 - nested_crossproduct
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341 - flat_crossproduct
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342
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343
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344 - name: WorkflowStep
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345 type: record
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346 docParent: "#Workflow"
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347 doc: |
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348 A workflow step is an executable element of a workflow. It specifies the
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349 underlying process implementation (such as `CommandLineTool` or another
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350 `Workflow`) in the `run` field and connects the input and output parameters
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351 of the underlying process to workflow parameters.
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352
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353 # Scatter/gather
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354
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355 To use scatter/gather,
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356 [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified
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357 in the workflow or workflow step requirements.
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358
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359 A "scatter" operation specifies that the associated workflow step or
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360 subworkflow should execute separately over a list of input elements. Each
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361 job making up a scatter operation is independent and may be executed
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362 concurrently.
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363
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364 The `scatter` field specifies one or more input parameters which will be
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365 scattered. An input parameter may be listed more than once. The declared
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366 type of each input parameter is implicitly becomes an array of items of the
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367 input parameter type. If a parameter is listed more than once, it becomes
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368 a nested array. As a result, upstream parameters which are connected to
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369 scattered parameters must be arrays.
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370
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371 All output parameter types are also implicitly wrapped in arrays. Each job
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372 in the scatter results in an entry in the output array.
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373
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374 If any scattered parameter runtime value is an empty array, all outputs are
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375 set to empty arrays and no work is done for the step, according to
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376 applicable scattering rules.
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377
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378 If `scatter` declares more than one input parameter, `scatterMethod`
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379 describes how to decompose the input into a discrete set of jobs.
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380
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381 * **dotproduct** specifies that each of the input arrays are aligned and one
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382 element taken from each array to construct each job. It is an error
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383 if all input arrays are not the same length.
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384
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385 * **nested_crossproduct** specifies the Cartesian product of the inputs,
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386 producing a job for every combination of the scattered inputs. The
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387 output must be nested arrays for each level of scattering, in the
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388 order that the input arrays are listed in the `scatter` field.
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389
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390 * **flat_crossproduct** specifies the Cartesian product of the inputs,
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391 producing a job for every combination of the scattered inputs. The
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392 output arrays must be flattened to a single level, but otherwise listed in the
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393 order that the input arrays are listed in the `scatter` field.
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394
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395 # Subworkflows
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396
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397 To specify a nested workflow as part of a workflow step,
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398 [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be
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399 specified in the workflow or workflow step requirements.
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400
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401 It is a fatal error if a workflow directly or indirectly invokes itself as
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402 a subworkflow (recursive workflows are not allowed).
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403
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404 fields:
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405 - name: id
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406 type: string
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407 jsonldPredicate: "@id"
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408 doc: "The unique identifier for this workflow step."
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409 - name: in
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410 type: WorkflowStepInput[]
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411 jsonldPredicate:
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412 _id: "cwl:in"
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413 mapSubject: id
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414 mapPredicate: source
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415 doc: |
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416 Defines the input parameters of the workflow step. The process is ready to
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417 run when all required input parameters are associated with concrete
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418 values. Input parameters include a schema for each parameter which is
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419 used to validate the input object. It may also be used build a user
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420 interface for constructing the input object.
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421 - name: out
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422 type:
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423 - type: array
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424 items: [string, WorkflowStepOutput]
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425 jsonldPredicate:
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426 _id: "cwl:out"
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427 _type: "@id"
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428 identity: true
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429 doc: |
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430 Defines the parameters representing the output of the process. May be
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431 used to generate and/or validate the output object.
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432 - name: requirements
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433 type: ProcessRequirement[]?
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434 jsonldPredicate:
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435 _id: "cwl:requirements"
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436 mapSubject: class
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437 doc: |
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438 Declares requirements that apply to either the runtime environment or the
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439 workflow engine that must be met in order to execute this workflow step. If
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440 an implementation cannot satisfy all requirements, or a requirement is
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441 listed which is not recognized by the implementation, it is a fatal
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442 error and the implementation must not attempt to run the process,
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443 unless overridden at user option.
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444 - name: hints
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445 type: Any[]?
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446 jsonldPredicate:
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447 _id: "cwl:hints"
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448 noLinkCheck: true
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449 mapSubject: class
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450 doc: |
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451 Declares hints applying to either the runtime environment or the
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452 workflow engine that may be helpful in executing this workflow step. It is
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453 not an error if an implementation cannot satisfy all hints, however
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454 the implementation may report a warning.
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455 - name: label
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456 type: string?
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457 jsonldPredicate: "rdfs:label"
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458 doc: "A short, human-readable label of this process object."
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459 - name: doc
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460 type: string?
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461 jsonldPredicate: "rdfs:comment"
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462 doc: "A long, human-readable description of this process object."
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463 - name: run
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464 type: [string, Process]
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465 jsonldPredicate:
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466 "_id": "cwl:run"
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467 "_type": "@id"
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468 doc: |
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469 Specifies the process to run.
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470 - name: scatter
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471 type:
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472 - string?
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473 - string[]?
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474 jsonldPredicate:
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475 "_id": "cwl:scatter"
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476 "_type": "@id"
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477 "_container": "@list"
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478 refScope: 0
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479 - name: scatterMethod
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480 doc: |
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481 Required if `scatter` is an array of more than one element.
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482 type: ScatterMethod?
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483 jsonldPredicate:
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484 "_id": "cwl:scatterMethod"
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485 "_type": "@vocab"
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486
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487
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488 - name: Workflow
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489 type: record
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490 extends: "#Process"
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491 documentRoot: true
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492 specialize:
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493 - specializeFrom: "#OutputParameter"
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494 specializeTo: "#WorkflowOutputParameter"
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495 doc: |
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496 A workflow describes a set of **steps** and the **dependencies** between
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497 those steps. When a step produces output that will be consumed by a
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498 second step, the first step is a dependency of the second step.
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499
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500 When there is a dependency, the workflow engine must execute the preceeding
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501 step and wait for it to successfully produce output before executing the
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502 dependent step. If two steps are defined in the workflow graph that
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503 are not directly or indirectly dependent, these steps are **independent**,
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504 and may execute in any order or execute concurrently. A workflow is
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505 complete when all steps have been executed.
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506
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507 Dependencies between parameters are expressed using the `source` field on
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508 [workflow step input parameters](#WorkflowStepInput) and [workflow output
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509 parameters](#WorkflowOutputParameter).
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510
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511 The `source` field expresses the dependency of one parameter on another
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512 such that when a value is associated with the parameter specified by
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513 `source`, that value is propagated to the destination parameter. When all
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514 data links inbound to a given step are fufilled, the step is ready to
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515 execute.
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516
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517 ## Workflow success and failure
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518
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519 A completed step must result in one of `success`, `temporaryFailure` or
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520 `permanentFailure` states. An implementation may choose to retry a step
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521 execution which resulted in `temporaryFailure`. An implementation may
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522 choose to either continue running other steps of a workflow, or terminate
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523 immediately upon `permanentFailure`.
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524
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525 * If any step of a workflow execution results in `permanentFailure`, then
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526 the workflow status is `permanentFailure`.
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527
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528 * If one or more steps result in `temporaryFailure` and all other steps
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529 complete `success` or are not executed, then the workflow status is
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530 `temporaryFailure`.
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531
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532 * If all workflow steps are executed and complete with `success`, then the
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533 workflow status is `success`.
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534
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535 # Extensions
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536
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537 [ScatterFeatureRequirement](#ScatterFeatureRequirement) and
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538 [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are
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539 available as standard [extensions](#Extensions_and_Metadata) to core
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540 workflow semantics.
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541
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542 fields:
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543 - name: "class"
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544 jsonldPredicate:
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545 "_id": "@type"
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546 "_type": "@vocab"
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547 type: string
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548 - name: steps
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549 doc: |
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550 The individual steps that make up the workflow. Each step is executed when all of its
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551 input data links are fufilled. An implementation may choose to execute
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552 the steps in a different order than listed and/or execute steps
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553 concurrently, provided that dependencies between steps are met.
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554 type:
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555 - type: array
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556 items: "#WorkflowStep"
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557 jsonldPredicate:
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558 mapSubject: id
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559
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560
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561 - type: record
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562 name: SubworkflowFeatureRequirement
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563 extends: ProcessRequirement
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564 doc: |
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565 Indicates that the workflow platform must support nested workflows in
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566 the `run` field of [WorkflowStep](#WorkflowStep).
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567 fields:
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568 - name: "class"
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569 type: "string"
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570 doc: "Always 'SubworkflowFeatureRequirement'"
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571 jsonldPredicate:
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572 "_id": "@type"
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573 "_type": "@vocab"
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574
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575 - name: ScatterFeatureRequirement
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576 type: record
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577 extends: ProcessRequirement
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578 doc: |
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579 Indicates that the workflow platform must support the `scatter` and
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580 `scatterMethod` fields of [WorkflowStep](#WorkflowStep).
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581 fields:
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582 - name: "class"
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583 type: "string"
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584 doc: "Always 'ScatterFeatureRequirement'"
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585 jsonldPredicate:
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586 "_id": "@type"
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587 "_type": "@vocab"
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588
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589 - name: MultipleInputFeatureRequirement
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590 type: record
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591 extends: ProcessRequirement
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592 doc: |
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593 Indicates that the workflow platform must support multiple inbound data links
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594 listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).
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595 fields:
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596 - name: "class"
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597 type: "string"
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598 doc: "Always 'MultipleInputFeatureRequirement'"
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599 jsonldPredicate:
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600 "_id": "@type"
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601 "_type": "@vocab"
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602
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603 - type: record
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604 name: StepInputExpressionRequirement
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605 extends: ProcessRequirement
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606 doc: |
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607 Indicate that the workflow platform must support the `valueFrom` field
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608 of [WorkflowStepInput](#WorkflowStepInput).
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609 fields:
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610 - name: "class"
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611 type: "string"
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612 doc: "Always 'StepInputExpressionRequirement'"
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613 jsonldPredicate:
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614 "_id": "@type"
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615 "_type": "@vocab"