annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.1.0-dev1/Workflow.yml @ 0:4f3585e2f14b draft default tip

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date Mon, 22 Mar 2021 18:12:50 +0000
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1 saladVersion: v1.1
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2 $base: "https://w3id.org/cwl/cwl#"
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3
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4 $namespaces:
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5 cwl: "https://w3id.org/cwl/cwl#"
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6 rdfs: "http://www.w3.org/2000/01/rdf-schema#"
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7
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8 $graph:
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9
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10 - name: "WorkflowDoc"
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11 type: documentation
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12 doc:
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13 - |
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14 # Common Workflow Language (CWL) Workflow Description, v1.1.0-dev1
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15
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16 This version:
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17 * https://w3id.org/cwl/v1.1.0-dev1/
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18
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19 Current version:
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20 * https://w3id.org/cwl/
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21 - "\n\n"
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22 - {$include: contrib.md}
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23 - "\n\n"
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24 - |
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25 # Abstract
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26
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27 One way to define a workflow is: an analysis task represented by a
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28 directed graph describing a sequence of operations that transform an
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29 input data set to output. This specification defines the Common Workflow
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30 Language (CWL) Workflow description, a vendor-neutral standard for
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31 representing workflows intended to be portable across a variety of
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32 computing platforms.
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33
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34 - {$include: intro.md}
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35
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36 - |
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37
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38 ## Introduction to CWL Workflow standard v1.1.0-dev1
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39
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40 This specification represents the latest stable release from the
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41 CWL group. Since the v1.0 release, v1.1.0-dev1 introduces the
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42 following updates to the CWL Workflow standard.
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43 Documents should to use `cwlVersion: v1.1.0-dev1` to make use of new
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44 syntax and features introduced in v1.1.0-dev1. Existing v1.0 documents
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45 should be trivially updatable by changing `cwlVersion`, however
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46 CWL documents that relied on previously undefined or
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47 underspecified behavior may have slightly different behavior in
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48 v1.1.0-dev1.
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49
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50 ## Changelog
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51
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52 * Clarify intent of ExpressionTool and clarify that they can be run standalone.
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53 * Clarify how Requirements are inherited by step processes.
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54 * Clarify behavior around step inputs not consumed by the target
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55 run process.
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56 * Document explicitly that CWL allows pass-through of workflow inputs to outputs.
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57 * Added optional name and doc fields to `OutputRecordSchema`.
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58 * Default values for some fields are now expressed in the schema.
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59 * When defining record types, fields of type `File` may now include
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60 `format`, `secondaryFiles`, and `streamable`.
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61 * The `Input` schemas (`Record`, `Array`, `Enum`), now permits a `doc` field.
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62 * Any `doc` field may be an array of strings in addition to the
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63 previously allowed single string.
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64 * The `run` field now introduces a subscope so that embedded
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65 definitions do not have identifier conflicts with the
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66 outer workflow.
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67 * `Workflow.inputs` and `ExpressionTool.inputs` now refer to the type
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68 `WorkflowInputParameter` instead of `InputParameter`; the only syntax
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69 difference from v1.0 is that `inputBinding` is now deprecated (as
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70 there is no command line to bind input values to) and `inputBinding`
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71 in a `Workflow` context will be removed in v2.0. Use the new
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72 `WorkflowInputParameter.loadContents` instead.
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73 * The presence of `OutputRecordField.outputBinding` in v1.0 was due to
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74 a technical error and as it makes no semantic sense it was removed.
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75 * `WorkflowStepInput` now has a `label` field.
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76 * [Addition](#Requirements_and_hints) of `cwl:requirements` field to
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77 input object documents.
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78 * `secondaryFiles` can now be explicitly marked as `required` or not.
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79 * Add note that undefined details related to execution are left open to
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80 the platform.
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81 * [Added](#WorkReuse) `WorkReuse` feature, allowing to enable or disable the reuse
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82 behavior for a particular tool or step for implementations that
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83 support reusing output from past work.
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84 * [Added](#NetworkAccess) `NetworkAccess` feature, allowing to indicate whether a
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85 process requires outgoing network access.
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86 * [Added](#InplaceUpdateRequirement) `InplaceUpdateRequirement` feature, allowing tools to directly
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87 update files with `writable: true` in `InitialWorkDirRequirement`.
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88 * [Added](#LoadListingRequirement) `LoadListingRequirement`
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89 and [loadListing](#LoadContents) to control whether and how
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90 `Directory` listings should be loaded for use in expressions.
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91 * [Better explain](#map) the `map<…>` notation that has existed since v1.0.
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92 * Fixed schema error where the `type` field inside the `inputs` and
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93 `outputs` fields for both `Workflow` and `ExpressionTool` was
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94 incorrectly listed as optional.
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95 * For multi-Process CWL documents, if no particular process is named then
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96 the process with the `id` of `#main` is chosen.
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97
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98 See also the [CWL Command Line Tool Description, v1.1.0-dev1 changelog](CommandLineTool.html#Changelog).
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99
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100 ## Purpose
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101
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102 The Common Workflow Language Command Line Tool Description express
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103 workflows for data-intensive science, such as Bioinformatics, Chemistry,
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104 Physics, and Astronomy. This specification is intended to define a data
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105 and execution model for Workflows that can be implemented on top of a
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106 variety of computing platforms, ranging from an individual workstation to
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107 cluster, grid, cloud, and high performance computing systems. Details related
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108 to execution of these workflow not laid out in this specification are open to
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109 interpretation by the computing platform implementing this specification.
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110
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111 - {$include: concepts.md}
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112
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113 - name: ExpressionToolOutputParameter
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114 type: record
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115 extends: OutputParameter
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116 fields:
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117 - name: type
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118 type:
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119 - CWLType
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120 - OutputRecordSchema
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121 - OutputEnumSchema
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122 - OutputArraySchema
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123 - string
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124 - type: array
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125 items:
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126 - CWLType
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127 - OutputRecordSchema
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128 - OutputEnumSchema
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129 - OutputArraySchema
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130 - string
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131 jsonldPredicate:
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132 "_id": "sld:type"
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133 "_type": "@vocab"
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134 refScope: 2
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135 typeDSL: True
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136 doc: |
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137 Specify valid types of data that may be assigned to this parameter.
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138
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139
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140 - name: WorkflowInputParameter
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141 type: record
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142 extends: InputParameter
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143 docParent: "#Workflow"
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144 fields:
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145 - name: type
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146 type:
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147 - CWLType
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148 - InputRecordSchema
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149 - InputEnumSchema
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150 - InputArraySchema
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151 - string
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152 - type: array
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153 items:
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154 - CWLType
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155 - InputRecordSchema
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156 - InputEnumSchema
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157 - InputArraySchema
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158 - string
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159 jsonldPredicate:
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160 "_id": "sld:type"
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161 "_type": "@vocab"
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162 refScope: 2
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163 typeDSL: True
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164 doc: |
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165 Specify valid types of data that may be assigned to this parameter.
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166 - name: inputBinding
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167 type: InputBinding?
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168 doc: |
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169 Deprecated. Preserved for v1.0 backwards compatability. Will be removed in
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170 CWL v2.0. Use `WorkflowInputParameter.loadContents` instead.
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171 jsonldPredicate: "cwl:inputBinding"
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172
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173
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174 - type: record
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175 name: ExpressionTool
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176 extends: Process
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177 specialize:
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178 - specializeFrom: InputParameter
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179 specializeTo: WorkflowInputParameter
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180 - specializeFrom: OutputParameter
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181 specializeTo: ExpressionToolOutputParameter
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182 documentRoot: true
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183 doc: |
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184 An ExpressionTool is a type of Process object that can be run by itself
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185 or as a Workflow step. It executes a pure Javascript expression that has
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186 access to the same input parameters as a workflow. It is meant to be used
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187 sparingly as a way to isolate complex Javascript expressions that need to
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188 operate on input data and produce some result; perhaps just a
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189 rearrangement of the inputs. No Docker software container is required
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190 or allowed.
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191 fields:
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192 - name: class
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193 jsonldPredicate:
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194 "_id": "@type"
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195 "_type": "@vocab"
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196 type: string
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197 - name: expression
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198 type: [string, Expression]
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199 doc: |
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200 The expression to execute. The expression must return a JSON object which
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201 matches the output parameters of the ExpressionTool.
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202
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203 - name: LinkMergeMethod
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204 type: enum
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205 docParent: "#WorkflowStepInput"
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206 doc: The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput).
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207 symbols:
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208 - merge_nested
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209 - merge_flattened
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210
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211
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212 - name: WorkflowOutputParameter
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213 type: record
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214 extends: OutputParameter
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215 docParent: "#Workflow"
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216 doc: |
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217 Describe an output parameter of a workflow. The parameter must be
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218 connected to one or more parameters defined in the workflow that
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219 will provide the value of the output parameter. It is legal to
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220 connect a WorkflowInputParameter to a WorkflowOutputParameter.
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221 fields:
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222 - name: outputSource
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223 doc: |
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224 Specifies one or more workflow parameters that supply the value of to
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225 the output parameter.
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226 jsonldPredicate:
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227 "_id": "cwl:outputSource"
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228 "_type": "@id"
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229 refScope: 0
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230 type:
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231 - string?
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232 - string[]?
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233 - name: linkMerge
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234 type: ["null", LinkMergeMethod]
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235 jsonldPredicate: "cwl:linkMerge"
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236 default: merge_nested
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237 doc: |
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238 The method to use to merge multiple sources into a single array.
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239 If not specified, the default method is "merge_nested".
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240 - name: type
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241 type:
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242 - CWLType
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243 - OutputRecordSchema
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244 - OutputEnumSchema
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245 - OutputArraySchema
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246 - string
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247 - type: array
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248 items:
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249 - CWLType
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250 - OutputRecordSchema
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251 - OutputEnumSchema
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252 - OutputArraySchema
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253 - string
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254 jsonldPredicate:
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255 "_id": "sld:type"
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256 "_type": "@vocab"
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257 refScope: 2
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258 typeDSL: True
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259 doc: |
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260 Specify valid types of data that may be assigned to this parameter.
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261
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262
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263 - name: Sink
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264 type: record
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265 abstract: true
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266 fields:
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267 - name: source
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268 doc: |
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269 Specifies one or more workflow parameters that will provide input to
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270 the underlying step parameter.
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271 jsonldPredicate:
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272 "_id": "cwl:source"
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273 "_type": "@id"
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274 refScope: 2
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275 type:
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276 - string?
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277 - string[]?
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278 - name: linkMerge
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279 type: LinkMergeMethod?
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280 jsonldPredicate: "cwl:linkMerge"
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281 default: merge_nested
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282 doc: |
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283 The method to use to merge multiple inbound links into a single array.
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284 If not specified, the default method is "merge_nested".
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285
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286
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287 - type: record
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288 name: WorkflowStepInput
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289 extends: [Identified, Sink, LoadContents, Labeled]
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290 docParent: "#WorkflowStep"
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291 doc: |
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292 The input of a workflow step connects an upstream parameter (from the
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293 workflow inputs, or the outputs of other workflows steps) with the input
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294 parameters of the process specified by the `run` field. Only input parameters
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295 declared by the target process will be passed through at runtime to the process
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296 though additonal parameters may be specified (for use within `valueFrom`
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297 expressions for instance) - unconnected or unused parameters do not represent an
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298 error condition.
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299
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300 ## Input object
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301
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302 A WorkflowStepInput object must contain an `id` field in the form
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303 `#fieldname` or `#prefix/fieldname`. When the `id` field contains a slash
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304 `/` the field name consists of the characters following the final slash
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305 (the prefix portion may contain one or more slashes to indicate scope).
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306 This defines a field of the workflow step input object with the value of
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307 the `source` parameter(s).
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308
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309 ## Merging
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310
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311 To merge multiple inbound data links,
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312 [MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified
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313 in the workflow or workflow step requirements.
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314
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315 If the sink parameter is an array, or named in a [workflow
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316 scatter](#WorkflowStep) operation, there may be multiple inbound data links
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317 listed in the `source` field. The values from the input links are merged
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318 depending on the method specified in the `linkMerge` field. If not
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319 specified, the default method is "merge_nested".
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320
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321 * **merge_nested**
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322
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323 The input must be an array consisting of exactly one entry for each
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324 input link. If "merge_nested" is specified with a single link, the value
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325 from the link must be wrapped in a single-item list.
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326
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327 * **merge_flattened**
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328
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329 1. The source and sink parameters must be compatible types, or the source
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330 type must be compatible with single element from the "items" type of
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331 the destination array parameter.
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332 2. Source parameters which are arrays are concatenated.
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333 Source parameters which are single element types are appended as
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334 single elements.
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335
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336 fields:
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337 - name: default
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338 type: ["null", Any]
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339 doc: |
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340 The default value for this parameter to use if either there is no
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341 `source` field, or the value produced by the `source` is `null`. The
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342 default must be applied prior to scattering or evaluating `valueFrom`.
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343 jsonldPredicate:
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344 _id: "sld:default"
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345 noLinkCheck: true
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346 - name: valueFrom
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347 type:
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348 - "null"
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349 - string
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350 - Expression
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351 jsonldPredicate: "cwl:valueFrom"
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352 doc: |
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353 To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must
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354 be specified in the workflow or workflow step requirements.
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355
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356 If `valueFrom` is a constant string value, use this as the value for
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357 this input parameter.
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358
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359 If `valueFrom` is a parameter reference or expression, it must be
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360 evaluated to yield the actual value to be assiged to the input field.
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361
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362 The `self` value in the parameter reference or expression must be
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363 1. `null` if there is no `source` field
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364 2. the value of the parameter(s) specified in the `source` field when this
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365 workflow input parameter **is not** specified in this workflow step's `scatter` field.
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366 3. an element of the parameter specified in the `source` field when this workflow input
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367 parameter **is** specified in this workflow step's `scatter` field.
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368
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369 The value of `inputs` in the parameter reference or expression must be
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370 the input object to the workflow step after assigning the `source`
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371 values, applying `default`, and then scattering. The order of
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372 evaluating `valueFrom` among step input parameters is undefined and the
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373 result of evaluating `valueFrom` on a parameter must not be visible to
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374 evaluation of `valueFrom` on other parameters.
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375
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376
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377 - type: record
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378 name: WorkflowStepOutput
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379 docParent: "#WorkflowStep"
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380 extends: Identified
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381 doc: |
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382 Associate an output parameter of the underlying process with a workflow
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383 parameter. The workflow parameter (given in the `id` field) be may be used
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384 as a `source` to connect with input parameters of other workflow steps, or
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385 with an output parameter of the process.
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386
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387 A unique identifier for this workflow output parameter. This is
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388 the identifier to use in the `source` field of `WorkflowStepInput`
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389 to connect the output value to downstream parameters.
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390
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391
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392 - name: ScatterMethod
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393 type: enum
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394 docParent: "#WorkflowStep"
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395 doc: The scatter method, as described in [workflow step scatter](#WorkflowStep).
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396 symbols:
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397 - dotproduct
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398 - nested_crossproduct
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399 - flat_crossproduct
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400
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401
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402 - name: WorkflowStep
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403 type: record
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404 extends: [Identified, Labeled, sld:Documented]
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405 docParent: "#Workflow"
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406 doc: |
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407 A workflow step is an executable element of a workflow. It specifies the
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408 underlying process implementation (such as `CommandLineTool` or another
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409 `Workflow`) in the `run` field and connects the input and output parameters
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410 of the underlying process to workflow parameters.
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411
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412 # Scatter/gather
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413
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414 To use scatter/gather,
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415 [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified
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416 in the workflow or workflow step requirements.
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417
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418 A "scatter" operation specifies that the associated workflow step or
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419 subworkflow should execute separately over a list of input elements. Each
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420 job making up a scatter operation is independent and may be executed
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421 concurrently.
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422
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423 The `scatter` field specifies one or more input parameters which will be
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424 scattered. An input parameter may be listed more than once. The declared
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425 type of each input parameter is implicitly becomes an array of items of the
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426 input parameter type. If a parameter is listed more than once, it becomes
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427 a nested array. As a result, upstream parameters which are connected to
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428 scattered parameters must be arrays.
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429
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430 All output parameter types are also implicitly wrapped in arrays. Each job
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431 in the scatter results in an entry in the output array.
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432
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433 If any scattered parameter runtime value is an empty array, all outputs are
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434 set to empty arrays and no work is done for the step, according to
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435 applicable scattering rules.
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436
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437 If `scatter` declares more than one input parameter, `scatterMethod`
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438 describes how to decompose the input into a discrete set of jobs.
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439
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440 * **dotproduct** specifies that each of the input arrays are aligned and one
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441 element taken from each array to construct each job. It is an error
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442 if all input arrays are not the same length.
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443
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444 * **nested_crossproduct** specifies the Cartesian product of the inputs,
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445 producing a job for every combination of the scattered inputs. The
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446 output must be nested arrays for each level of scattering, in the
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447 order that the input arrays are listed in the `scatter` field.
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448
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449 * **flat_crossproduct** specifies the Cartesian product of the inputs,
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450 producing a job for every combination of the scattered inputs. The
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451 output arrays must be flattened to a single level, but otherwise listed in the
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452 order that the input arrays are listed in the `scatter` field.
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453
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454 # Subworkflows
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455
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456 To specify a nested workflow as part of a workflow step,
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457 [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be
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458 specified in the workflow or workflow step requirements.
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459
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460 It is a fatal error if a workflow directly or indirectly invokes itself as
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461 a subworkflow (recursive workflows are not allowed).
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462
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463 fields:
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464 - name: in
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465 type: WorkflowStepInput[]
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466 jsonldPredicate:
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467 _id: "cwl:in"
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468 mapSubject: id
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469 mapPredicate: source
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470 doc: |
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471 Defines the input parameters of the workflow step. The process is ready to
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472 run when all required input parameters are associated with concrete
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473 values. Input parameters include a schema for each parameter which is
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474 used to validate the input object. It may also be used build a user
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475 interface for constructing the input object.
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476 - name: out
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477 type:
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478 - type: array
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479 items: [string, WorkflowStepOutput]
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480 jsonldPredicate:
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481 _id: "cwl:out"
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482 _type: "@id"
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483 identity: true
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484 doc: |
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485 Defines the parameters representing the output of the process. May be
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486 used to generate and/or validate the output object.
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487 - name: requirements
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488 type: ProcessRequirement[]?
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489 jsonldPredicate:
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490 _id: "cwl:requirements"
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491 mapSubject: class
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492 doc: |
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493 Declares requirements that apply to either the runtime environment or the
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494 workflow engine that must be met in order to execute this workflow step. If
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495 an implementation cannot satisfy all requirements, or a requirement is
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496 listed which is not recognized by the implementation, it is a fatal
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497 error and the implementation must not attempt to run the process,
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498 unless overridden at user option.
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499 - name: hints
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500 type: Any[]?
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501 jsonldPredicate:
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502 _id: "cwl:hints"
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503 noLinkCheck: true
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504 mapSubject: class
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505 doc: |
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506 Declares hints applying to either the runtime environment or the
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507 workflow engine that may be helpful in executing this workflow step. It is
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508 not an error if an implementation cannot satisfy all hints, however
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509 the implementation may report a warning.
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510 - name: run
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511 type: [string, Process]
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512 jsonldPredicate:
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513 _id: "cwl:run"
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514 _type: "@id"
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515 subscope: run
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516 doc: |
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517 Specifies the process to run.
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518 - name: scatter
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519 type:
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520 - string?
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521 - string[]?
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522 jsonldPredicate:
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523 "_id": "cwl:scatter"
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524 "_type": "@id"
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525 "_container": "@list"
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526 refScope: 0
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527 - name: scatterMethod
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528 doc: |
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529 Required if `scatter` is an array of more than one element.
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530 type: ScatterMethod?
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531 jsonldPredicate:
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532 "_id": "cwl:scatterMethod"
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533 "_type": "@vocab"
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534
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535
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536 - name: Workflow
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537 type: record
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538 extends: "#Process"
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539 documentRoot: true
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540 specialize:
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541 - specializeFrom: InputParameter
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542 specializeTo: WorkflowInputParameter
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543 - specializeFrom: OutputParameter
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544 specializeTo: WorkflowOutputParameter
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545 doc: |
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546 A workflow describes a set of **steps** and the **dependencies** between
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547 those steps. When a step produces output that will be consumed by a
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548 second step, the first step is a dependency of the second step.
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549
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550 When there is a dependency, the workflow engine must execute the preceeding
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551 step and wait for it to successfully produce output before executing the
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552 dependent step. If two steps are defined in the workflow graph that
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553 are not directly or indirectly dependent, these steps are **independent**,
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554 and may execute in any order or execute concurrently. A workflow is
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555 complete when all steps have been executed.
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556
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557 Dependencies between parameters are expressed using the `source` field on
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558 [workflow step input parameters](#WorkflowStepInput) and [workflow output
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559 parameters](#WorkflowOutputParameter).
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560
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561 The `source` field expresses the dependency of one parameter on another
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562 such that when a value is associated with the parameter specified by
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563 `source`, that value is propagated to the destination parameter. When all
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564 data links inbound to a given step are fufilled, the step is ready to
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565 execute.
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566
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567 ## Workflow success and failure
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568
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569 A completed step must result in one of `success`, `temporaryFailure` or
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570 `permanentFailure` states. An implementation may choose to retry a step
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571 execution which resulted in `temporaryFailure`. An implementation may
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572 choose to either continue running other steps of a workflow, or terminate
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573 immediately upon `permanentFailure`.
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574
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575 * If any step of a workflow execution results in `permanentFailure`, then
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576 the workflow status is `permanentFailure`.
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577
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578 * If one or more steps result in `temporaryFailure` and all other steps
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579 complete `success` or are not executed, then the workflow status is
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580 `temporaryFailure`.
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581
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582 * If all workflow steps are executed and complete with `success`, then the
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583 workflow status is `success`.
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584
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585 # Extensions
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586
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587 [ScatterFeatureRequirement](#ScatterFeatureRequirement) and
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588 [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are
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589 available as standard [extensions](#Extensions_and_Metadata) to core
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590 workflow semantics.
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591
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592 fields:
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593 - name: "class"
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594 jsonldPredicate:
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595 "_id": "@type"
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596 "_type": "@vocab"
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597 type: string
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598 - name: steps
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599 doc: |
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600 The individual steps that make up the workflow. Each step is executed when all of its
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601 input data links are fufilled. An implementation may choose to execute
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602 the steps in a different order than listed and/or execute steps
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603 concurrently, provided that dependencies between steps are met.
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604 type:
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605 - type: array
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606 items: "#WorkflowStep"
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607 jsonldPredicate:
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608 mapSubject: id
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609
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610
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611 - type: record
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612 name: SubworkflowFeatureRequirement
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613 extends: ProcessRequirement
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614 doc: |
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615 Indicates that the workflow platform must support nested workflows in
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616 the `run` field of [WorkflowStep](#WorkflowStep).
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617 fields:
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618 - name: "class"
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619 type: "string"
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620 doc: "Always 'SubworkflowFeatureRequirement'"
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621 jsonldPredicate:
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622 "_id": "@type"
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623 "_type": "@vocab"
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624
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625 - name: ScatterFeatureRequirement
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626 type: record
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627 extends: ProcessRequirement
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628 doc: |
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629 Indicates that the workflow platform must support the `scatter` and
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630 `scatterMethod` fields of [WorkflowStep](#WorkflowStep).
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631 fields:
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632 - name: "class"
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633 type: "string"
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634 doc: "Always 'ScatterFeatureRequirement'"
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635 jsonldPredicate:
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636 "_id": "@type"
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637 "_type": "@vocab"
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638
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639 - name: MultipleInputFeatureRequirement
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640 type: record
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641 extends: ProcessRequirement
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642 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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643 Indicates that the workflow platform must support multiple inbound data links
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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644 listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).
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645 fields:
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646 - name: "class"
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647 type: "string"
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648 doc: "Always 'MultipleInputFeatureRequirement'"
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649 jsonldPredicate:
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650 "_id": "@type"
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651 "_type": "@vocab"
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652
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653 - type: record
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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654 name: StepInputExpressionRequirement
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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655 extends: ProcessRequirement
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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656 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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657 Indicate that the workflow platform must support the `valueFrom` field
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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658 of [WorkflowStepInput](#WorkflowStepInput).
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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659 fields:
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660 - name: "class"
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661 type: "string"
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662 doc: "Always 'StepInputExpressionRequirement'"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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663 jsonldPredicate:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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664 "_id": "@type"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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665 "_type": "@vocab"