Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.2/Workflow.yml @ 0:4f3585e2f14b draft default tip
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author | shellac |
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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 $graph: |
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9 |
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10 - name: "WorkflowDoc" |
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11 type: documentation |
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12 doc: |
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13 - | |
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14 # Common Workflow Language (CWL) Workflow Description, v1.2 |
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15 |
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16 This version: |
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17 * https://w3id.org/cwl/v1.2/ |
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18 |
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19 Latest stable version: |
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20 * https://w3id.org/cwl/ |
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21 - "\n\n" |
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22 - {$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 This specification defines the Common Workflow Language (CWL) |
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28 Workflow description, a vendor-neutral standard for representing |
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29 analysis tasks where a sequence of operations are described |
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30 using a directed graph of operations to transform input to |
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31 output. CWL is portable across a variety of computing |
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32 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 v1.2 |
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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 v1.1 release, v1.2 introduces the |
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42 following updates to the CWL Workflow standard. |
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43 Documents should to use `cwlVersion: v1.2` to make use of new |
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44 syntax and features introduced in v1.2. Existing v1.1 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 v1.2. |
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49 |
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50 ## Changelog |
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51 |
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52 * Adds `when` field to [WorkflowStep](#WorkflowStep) for conditional |
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53 execution |
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54 * Adds `pickValue` field to [WorkflowStepInput](#WorkflowStepInput) and |
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55 [WorkflowOutputParameter](#WorkflowOutputParameter) for selecting among null and |
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56 non-null source values |
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57 * Add abstract [Operation](#Operation) that can be used as a |
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58 no-op stand-in to describe abstract workflows. |
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59 * [Workflow](#Workflow), [ExpressionTool](#ExpressionTool) and |
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60 [Operation](#Operation) can now express `intent` with an |
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61 identifier for the type of computational operation. |
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62 * Clarify there are no limits on the size of file literal `contents`. |
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63 * When using `loadContents` it now must fail when attempting to |
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64 load a file greater than 64 KiB instead of silently truncating |
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65 the data. |
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66 * Note that only enum and record types can be typedef-ed |
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67 * Escaping in [string interpolation](#String_Interpolation) has |
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68 been added to the specification along with conformance tests. |
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69 * Added discussion of [packed documents](#Packed_documents). |
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70 * Specify behavior when `source` is a single-item list and no |
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71 linkMerge is set. |
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72 * Added discussion about handling different document versions. |
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73 * Added definition of **data link** |
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74 |
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75 See also the [CWL Command Line Tool Description, v1.2 changelog](CommandLineTool.html#Changelog). |
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76 For other changes since CWL v1.0, see the |
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77 [CWL Workflow Description, v1.1 changelog](https://www.commonwl.org/v1.1/Workflow.html#Changelog) |
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78 |
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79 ## Purpose |
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80 |
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81 The Common Workflow Language Command Line Tool Description |
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82 express workflows for data-intensive science, such as |
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83 bioinformatics, physics, astronomy, geoscience, and machine |
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84 learning. This specification is intended to define a data and |
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85 execution model for Workflows that can be implemented on top of |
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86 a variety of computing platforms, ranging from an individual |
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87 workstation to cluster, grid, cloud, and high performance |
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88 computing systems. Details related to execution of these |
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89 workflow not laid out in this specification are open to |
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90 interpretation by the computing platform implementing this |
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91 specification. |
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92 |
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93 - {$include: concepts.md} |
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94 |
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95 - name: ExpressionToolOutputParameter |
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96 type: record |
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97 extends: OutputParameter |
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98 fields: |
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99 - name: type |
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100 type: |
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101 - CWLType |
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102 - OutputRecordSchema |
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103 - OutputEnumSchema |
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104 - OutputArraySchema |
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105 - string |
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106 - type: array |
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107 items: |
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108 - CWLType |
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109 - OutputRecordSchema |
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110 - OutputEnumSchema |
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111 - OutputArraySchema |
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112 - string |
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113 jsonldPredicate: |
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114 "_id": "sld:type" |
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115 "_type": "@vocab" |
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116 refScope: 2 |
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117 typeDSL: True |
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118 doc: | |
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119 Specify valid types of data that may be assigned to this parameter. |
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120 |
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121 |
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122 - name: WorkflowInputParameter |
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123 type: record |
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124 extends: InputParameter |
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125 docParent: "#Workflow" |
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126 fields: |
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127 - name: type |
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128 type: |
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129 - CWLType |
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130 - InputRecordSchema |
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131 - InputEnumSchema |
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132 - InputArraySchema |
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133 - string |
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134 - type: array |
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135 items: |
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136 - CWLType |
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137 - InputRecordSchema |
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138 - InputEnumSchema |
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139 - InputArraySchema |
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140 - string |
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141 jsonldPredicate: |
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142 "_id": "sld:type" |
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143 "_type": "@vocab" |
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144 refScope: 2 |
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145 typeDSL: True |
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146 doc: | |
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147 Specify valid types of data that may be assigned to this parameter. |
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148 - name: inputBinding |
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149 type: InputBinding? |
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150 doc: | |
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151 Deprecated. Preserved for v1.0 backwards compatability. Will be removed in |
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152 CWL v2.0. Use `WorkflowInputParameter.loadContents` instead. |
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153 jsonldPredicate: "cwl:inputBinding" |
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154 |
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155 |
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156 - type: record |
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157 name: ExpressionTool |
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158 extends: Process |
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159 specialize: |
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160 - specializeFrom: InputParameter |
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161 specializeTo: WorkflowInputParameter |
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162 - specializeFrom: OutputParameter |
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163 specializeTo: ExpressionToolOutputParameter |
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164 documentRoot: true |
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165 doc: | |
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166 An ExpressionTool is a type of Process object that can be run by itself |
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167 or as a Workflow step. It executes a pure Javascript expression that has |
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168 access to the same input parameters as a workflow. It is meant to be used |
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169 sparingly as a way to isolate complex Javascript expressions that need to |
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170 operate on input data and produce some result; perhaps just a |
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171 rearrangement of the inputs. No Docker software container is required |
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172 or allowed. |
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173 fields: |
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174 - name: class |
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175 jsonldPredicate: |
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176 "_id": "@type" |
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177 "_type": "@vocab" |
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178 type: string |
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179 - name: expression |
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180 type: Expression |
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181 doc: | |
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182 The expression to execute. The expression must return a plain |
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183 Javascript object which matches the output parameters of the |
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184 ExpressionTool. |
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185 |
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186 - name: LinkMergeMethod |
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187 type: enum |
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188 docParent: "#WorkflowStepInput" |
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189 doc: The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput). |
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190 symbols: |
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191 - merge_nested |
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192 - merge_flattened |
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193 |
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194 |
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195 - name: PickValueMethod |
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196 type: enum |
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197 docParent: "#WorkflowStepInput" |
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198 doc: | |
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199 Picking non-null values among inbound data links, described in [WorkflowStepInput](#WorkflowStepInput). |
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200 symbols: |
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201 - first_non_null |
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202 - the_only_non_null |
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203 - all_non_null |
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204 |
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205 |
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206 - name: WorkflowOutputParameter |
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207 type: record |
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208 extends: OutputParameter |
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209 docParent: "#Workflow" |
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210 doc: | |
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211 Describe an output parameter of a workflow. The parameter must be |
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212 connected to one or more parameters defined in the workflow that |
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213 will provide the value of the output parameter. It is legal to |
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214 connect a WorkflowInputParameter to a WorkflowOutputParameter. |
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215 |
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216 See [WorkflowStepInput](#WorkflowStepInput) for discussion of |
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217 `linkMerge` and `pickValue`. |
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218 fields: |
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219 - name: outputSource |
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220 doc: | |
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221 Specifies one or more workflow parameters that supply the value of to |
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222 the output parameter. |
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223 jsonldPredicate: |
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224 "_id": "cwl:outputSource" |
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225 "_type": "@id" |
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226 refScope: 0 |
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227 type: |
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228 - string? |
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229 - string[]? |
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230 - name: linkMerge |
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231 type: ["null", LinkMergeMethod] |
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232 jsonldPredicate: "cwl:linkMerge" |
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233 default: merge_nested |
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234 doc: | |
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235 The method to use to merge multiple sources into a single array. |
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236 If not specified, the default method is "merge_nested". |
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237 |
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238 - name: pickValue |
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239 type: ["null", PickValueMethod] |
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240 jsonldPredicate: "cwl:pickValue" |
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241 doc: | |
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242 The method to use to choose non-null elements among multiple sources. |
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243 |
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244 - name: type |
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245 type: |
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246 - CWLType |
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247 - OutputRecordSchema |
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248 - OutputEnumSchema |
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249 - OutputArraySchema |
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250 - string |
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251 - type: array |
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252 items: |
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253 - CWLType |
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254 - OutputRecordSchema |
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255 - OutputEnumSchema |
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256 - OutputArraySchema |
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257 - string |
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258 jsonldPredicate: |
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259 "_id": "sld:type" |
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260 "_type": "@vocab" |
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261 refScope: 2 |
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262 typeDSL: True |
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263 doc: | |
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264 Specify valid types of data that may be assigned to this parameter. |
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265 |
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266 |
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267 - name: Sink |
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268 type: record |
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269 abstract: true |
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270 fields: |
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271 - name: source |
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272 doc: | |
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273 Specifies one or more workflow parameters that will provide input to |
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274 the underlying step parameter. |
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275 jsonldPredicate: |
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276 "_id": "cwl:source" |
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277 "_type": "@id" |
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278 refScope: 2 |
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279 type: |
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280 - string? |
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281 - string[]? |
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282 - name: linkMerge |
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283 type: LinkMergeMethod? |
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284 jsonldPredicate: "cwl:linkMerge" |
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285 default: merge_nested |
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286 doc: | |
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287 The method to use to merge multiple inbound links into a single array. |
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288 If not specified, the default method is "merge_nested". |
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289 - name: pickValue |
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290 type: ["null", PickValueMethod] |
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291 jsonldPredicate: "cwl:pickValue" |
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292 doc: | |
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293 The method to use to choose non-null elements among multiple sources. |
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294 |
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295 |
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296 - type: record |
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297 name: WorkflowStepInput |
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298 extends: [Identified, Sink, LoadContents, Labeled] |
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299 docParent: "#WorkflowStep" |
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300 doc: | |
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301 The input of a workflow step connects an upstream parameter (from the |
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302 workflow inputs, or the outputs of other workflows steps) with the input |
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303 parameters of the process specified by the `run` field. Only input parameters |
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304 declared by the target process will be passed through at runtime to the process |
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305 though additonal parameters may be specified (for use within `valueFrom` |
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306 expressions for instance) - unconnected or unused parameters do not represent an |
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307 error condition. |
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308 |
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309 # Input object |
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310 |
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311 A WorkflowStepInput object must contain an `id` field in the form |
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312 `#fieldname` or `#prefix/fieldname`. When the `id` field contains a slash |
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313 `/` the field name consists of the characters following the final slash |
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314 (the prefix portion may contain one or more slashes to indicate scope). |
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315 This defines a field of the workflow step input object with the value of |
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316 the `source` parameter(s). |
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317 |
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318 # Merging multiple inbound data links |
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319 |
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320 To merge multiple inbound data links, |
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321 [MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified |
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322 in the workflow or workflow step requirements. |
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323 |
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324 If the sink parameter is an array, or named in a [workflow |
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325 scatter](#WorkflowStep) operation, there may be multiple inbound |
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326 data links listed in the `source` field. The values from the |
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327 input links are merged depending on the method specified in the |
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328 `linkMerge` field. If both `linkMerge` and `pickValue` are null |
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329 or not specified, and there is more than one element in the |
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330 `source` array, the default method is "merge_nested". |
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331 |
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332 If both `linkMerge` and `pickValue` are null or not specified, and |
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333 there is only a single element in the `source`, then the input |
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334 parameter takes the scalar value from the single input link (it is |
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335 *not* wrapped in a single-list). |
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336 |
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337 * **merge_nested** |
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338 |
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339 The input must be an array consisting of exactly one entry for each |
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340 input link. If "merge_nested" is specified with a single link, the value |
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341 from the link must be wrapped in a single-item list. |
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342 |
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343 * **merge_flattened** |
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344 |
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345 1. The source and sink parameters must be compatible types, or the source |
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346 type must be compatible with single element from the "items" type of |
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347 the destination array parameter. |
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348 2. Source parameters which are arrays are concatenated. |
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349 Source parameters which are single element types are appended as |
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350 single elements. |
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351 |
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352 # Picking non-null values among inbound data links |
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353 |
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354 If present, `pickValue` specifies how to picking non-null values among inbound data links. |
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355 |
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356 `pickValue` is evaluated |
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357 1. Once all source values from upstream step or parameters are available. |
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358 2. After `linkMerge`. |
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359 3. Before `scatter` or `valueFrom`. |
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360 |
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361 This is specifically intended to be useful in combination with |
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362 [conditional execution](#WorkflowStep), where several upstream |
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363 steps may be connected to a single input (`source` is a list), and |
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364 skipped steps produce null values. |
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365 |
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366 Static type checkers should check for type consistency after infering what the type |
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367 will be after `pickValue` is applied, just as they do currently for `linkMerge`. |
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368 |
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369 * **first_non_null** |
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370 |
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371 For the first level of a list input, pick the first non-null element. The result is a scalar. |
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372 It is an error if there is no non-null element. Examples: |
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373 * `[null, x, null, y] -> x` |
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374 * `[null, [null], null, y] -> [null]` |
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375 * `[null, null, null] -> Runtime Error` |
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376 |
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377 *Intended use case*: If-else pattern where the |
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378 value comes either from a conditional step or from a default or |
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379 fallback value. The conditional step(s) should be placed first in |
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380 the list. |
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381 |
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382 * **the_only_non_null** |
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383 |
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384 For the first level of a list input, pick the single non-null element. The result is a scalar. |
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385 It is an error if there is more than one non-null element. Examples: |
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386 |
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387 * `[null, x, null] -> x` |
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388 * `[null, x, null, y] -> Runtime Error` |
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389 * `[null, [null], null] -> [null]` |
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390 * `[null, null, null] -> Runtime Error` |
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391 |
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392 *Intended use case*: Switch type patterns where developer considers |
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393 more than one active code path as a workflow error |
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394 (possibly indicating an error in writing `when` condition expressions). |
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395 |
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396 * **all_non_null** |
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397 |
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398 For the first level of a list input, pick all non-null values. |
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399 The result is a list, which may be empty. Examples: |
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400 |
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401 * `[null, x, null] -> [x]` |
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402 * `[x, null, y] -> [x, y]` |
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403 * `[null, [x], [null]] -> [[x], [null]]` |
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404 * `[null, null, null] -> []` |
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405 |
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406 *Intended use case*: It is valid to have more than one source, but |
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407 sources are conditional, so null sources (from skipped steps) |
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408 should be filtered out. |
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409 |
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410 fields: |
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411 - name: default |
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412 type: ["null", Any] |
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413 doc: | |
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414 The default value for this parameter to use if either there is no |
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415 `source` field, or the value produced by the `source` is `null`. The |
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416 default must be applied prior to scattering or evaluating `valueFrom`. |
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417 jsonldPredicate: |
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418 _id: "sld:default" |
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419 noLinkCheck: true |
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420 - name: valueFrom |
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421 type: |
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422 - "null" |
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423 - string |
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424 - Expression |
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425 jsonldPredicate: "cwl:valueFrom" |
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426 doc: | |
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427 To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must |
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428 be specified in the workflow or workflow step requirements. |
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429 |
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430 If `valueFrom` is a constant string value, use this as the value for |
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431 this input parameter. |
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432 |
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433 If `valueFrom` is a parameter reference or expression, it must be |
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434 evaluated to yield the actual value to be assiged to the input field. |
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435 |
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436 The `self` value in the parameter reference or expression must be |
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437 1. `null` if there is no `source` field |
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438 2. the value of the parameter(s) specified in the `source` field when this |
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439 workflow input parameter **is not** specified in this workflow step's `scatter` field. |
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440 3. an element of the parameter specified in the `source` field when this workflow input |
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441 parameter **is** specified in this workflow step's `scatter` field. |
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442 |
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443 The value of `inputs` in the parameter reference or expression must be |
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444 the input object to the workflow step after assigning the `source` |
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445 values, applying `default`, and then scattering. The order of |
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446 evaluating `valueFrom` among step input parameters is undefined and the |
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447 result of evaluating `valueFrom` on a parameter must not be visible to |
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448 evaluation of `valueFrom` on other parameters. |
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449 |
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450 |
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451 - type: record |
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452 name: WorkflowStepOutput |
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453 docParent: "#WorkflowStep" |
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454 extends: Identified |
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455 doc: | |
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456 Associate an output parameter of the underlying process with a workflow |
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457 parameter. The workflow parameter (given in the `id` field) be may be used |
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458 as a `source` to connect with input parameters of other workflow steps, or |
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459 with an output parameter of the process. |
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460 |
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461 A unique identifier for this workflow output parameter. This is |
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462 the identifier to use in the `source` field of `WorkflowStepInput` |
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463 to connect the output value to downstream parameters. |
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464 |
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465 |
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466 - name: ScatterMethod |
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467 type: enum |
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468 docParent: "#WorkflowStep" |
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469 doc: The scatter method, as described in [workflow step scatter](#WorkflowStep). |
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470 symbols: |
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471 - dotproduct |
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472 - nested_crossproduct |
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473 - flat_crossproduct |
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474 |
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475 |
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476 - name: WorkflowStep |
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477 type: record |
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478 extends: [Identified, Labeled, sld:Documented] |
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479 docParent: "#Workflow" |
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480 doc: | |
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481 A workflow step is an executable element of a workflow. It specifies the |
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482 underlying process implementation (such as `CommandLineTool` or another |
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483 `Workflow`) in the `run` field and connects the input and output parameters |
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484 of the underlying process to workflow parameters. |
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485 |
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486 # Scatter/gather |
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487 |
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488 To use scatter/gather, |
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489 [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified |
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490 in the workflow or workflow step requirements. |
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491 |
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492 A "scatter" operation specifies that the associated workflow step or |
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493 subworkflow should execute separately over a list of input elements. Each |
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494 job making up a scatter operation is independent and may be executed |
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495 concurrently. |
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496 |
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497 The `scatter` field specifies one or more input parameters which will be |
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498 scattered. An input parameter may be listed more than once. The declared |
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499 type of each input parameter is implicitly becomes an array of items of the |
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500 input parameter type. If a parameter is listed more than once, it becomes |
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501 a nested array. As a result, upstream parameters which are connected to |
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502 scattered parameters must be arrays. |
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503 |
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504 All output parameter types are also implicitly wrapped in arrays. Each job |
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505 in the scatter results in an entry in the output array. |
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506 |
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507 If any scattered parameter runtime value is an empty array, all outputs are |
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508 set to empty arrays and no work is done for the step, according to |
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509 applicable scattering rules. |
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510 |
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511 If `scatter` declares more than one input parameter, `scatterMethod` |
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512 describes how to decompose the input into a discrete set of jobs. |
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513 |
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514 * **dotproduct** specifies that each of the input arrays are aligned and one |
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515 element taken from each array to construct each job. It is an error |
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516 if all input arrays are not the same length. |
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517 |
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518 * **nested_crossproduct** specifies the Cartesian product of the inputs, |
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519 producing a job for every combination of the scattered inputs. The |
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520 output must be nested arrays for each level of scattering, in the |
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521 order that the input arrays are listed in the `scatter` field. |
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522 |
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523 * **flat_crossproduct** specifies the Cartesian product of the inputs, |
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524 producing a job for every combination of the scattered inputs. The |
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525 output arrays must be flattened to a single level, but otherwise listed in the |
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526 order that the input arrays are listed in the `scatter` field. |
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527 |
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528 # Conditional execution (Optional) |
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529 |
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530 Conditional execution makes execution of a step conditional on an |
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531 expression. A step that is not executed is "skipped". A skipped |
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532 step produces `null` for all output parameters. |
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533 |
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534 The condition is evaluated after `scatter`, using the input object |
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535 of each individual scatter job. This means over a set of scatter |
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536 jobs, some may be executed and some may be skipped. When the |
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537 results are gathered, skipped steps must be `null` in the output |
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538 arrays. |
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539 |
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540 The `when` field controls conditional execution. This is an |
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541 expression that must be evaluated with `inputs` bound to the step |
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542 input object (or individual scatter job), and returns a boolean |
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543 value. It is an error if this expression returns a value other |
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544 than `true` or `false`. |
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545 |
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546 Conditionals in CWL are an optional feature and are not required |
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547 to be implemented by all consumers of CWL documents. An |
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548 implementation that does not support conditionals must return a |
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549 fatal error when attempting execute a workflow that uses |
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550 conditional constructs the implementation does not support. |
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551 |
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552 # Subworkflows |
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553 |
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554 To specify a nested workflow as part of a workflow step, |
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555 [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be |
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556 specified in the workflow or workflow step requirements. |
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557 |
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558 It is a fatal error if a workflow directly or indirectly invokes itself as |
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559 a subworkflow (recursive workflows are not allowed). |
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560 |
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561 fields: |
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562 - name: in |
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563 type: WorkflowStepInput[] |
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564 jsonldPredicate: |
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565 _id: "cwl:in" |
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566 mapSubject: id |
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567 mapPredicate: source |
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568 doc: | |
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569 Defines the input parameters of the workflow step. The process is ready to |
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570 run when all required input parameters are associated with concrete |
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571 values. Input parameters include a schema for each parameter which is |
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572 used to validate the input object. It may also be used build a user |
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573 interface for constructing the input object. |
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574 - name: out |
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575 type: |
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576 - type: array |
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577 items: [string, WorkflowStepOutput] |
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578 jsonldPredicate: |
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579 _id: "cwl:out" |
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580 _type: "@id" |
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581 identity: true |
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582 doc: | |
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583 Defines the parameters representing the output of the process. May be |
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584 used to generate and/or validate the output object. |
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585 - name: requirements |
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586 type: ProcessRequirement[]? |
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587 jsonldPredicate: |
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588 _id: "cwl:requirements" |
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589 mapSubject: class |
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590 doc: | |
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591 Declares requirements that apply to either the runtime environment or the |
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592 workflow engine that must be met in order to execute this workflow step. If |
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593 an implementation cannot satisfy all requirements, or a requirement is |
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594 listed which is not recognized by the implementation, it is a fatal |
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595 error and the implementation must not attempt to run the process, |
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596 unless overridden at user option. |
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597 - name: hints |
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598 type: Any[]? |
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599 jsonldPredicate: |
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600 _id: "cwl:hints" |
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601 noLinkCheck: true |
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602 mapSubject: class |
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603 doc: | |
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604 Declares hints applying to either the runtime environment or the |
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605 workflow engine that may be helpful in executing this workflow step. It is |
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606 not an error if an implementation cannot satisfy all hints, however |
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607 the implementation may report a warning. |
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608 - name: run |
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609 type: [string, Process] |
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610 jsonldPredicate: |
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611 _id: "cwl:run" |
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612 _type: "@id" |
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613 subscope: run |
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614 doc: | |
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615 Specifies the process to run. |
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616 - name: when |
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617 type: |
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618 - "null" |
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619 - Expression |
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620 jsonldPredicate: "cwl:when" |
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621 doc: | |
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622 If defined, only run the step when the expression evaluates to |
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623 `true`. If `false` the step is skipped. A skipped step |
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624 produces a `null` on each output. |
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625 - name: scatter |
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626 type: |
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627 - string? |
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628 - string[]? |
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629 jsonldPredicate: |
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630 "_id": "cwl:scatter" |
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631 "_type": "@id" |
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632 "_container": "@list" |
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633 refScope: 0 |
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634 - name: scatterMethod |
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635 doc: | |
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636 Required if `scatter` is an array of more than one element. |
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637 type: ScatterMethod? |
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638 jsonldPredicate: |
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639 "_id": "cwl:scatterMethod" |
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640 "_type": "@vocab" |
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641 |
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642 |
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643 - name: Workflow |
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644 type: record |
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645 extends: "#Process" |
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646 documentRoot: true |
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647 specialize: |
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648 - specializeFrom: InputParameter |
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649 specializeTo: WorkflowInputParameter |
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650 - specializeFrom: OutputParameter |
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651 specializeTo: WorkflowOutputParameter |
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652 doc: | |
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653 A workflow describes a set of **steps** and the **dependencies** between |
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654 those steps. When a step produces output that will be consumed by a |
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655 second step, the first step is a dependency of the second step. |
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656 |
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657 When there is a dependency, the workflow engine must execute the preceeding |
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658 step and wait for it to successfully produce output before executing the |
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659 dependent step. If two steps are defined in the workflow graph that |
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660 are not directly or indirectly dependent, these steps are **independent**, |
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661 and may execute in any order or execute concurrently. A workflow is |
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662 complete when all steps have been executed. |
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663 |
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664 Dependencies between parameters are expressed using the `source` |
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665 field on [workflow step input parameters](#WorkflowStepInput) and |
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666 `outputSource` field on [workflow output |
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667 parameters](#WorkflowOutputParameter). |
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668 |
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669 The `source` field on each workflow step input parameter expresses |
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670 the data links that contribute to the value of the step input |
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671 parameter (the "sink"). A workflow step can only begin execution |
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672 when every data link connected to a step has been fulfilled. |
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673 |
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674 The `outputSource` field on each workflow step input parameter |
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675 expresses the data links that contribute to the value of the |
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676 workflow output parameter (the "sink"). Workflow execution cannot |
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677 complete successfully until every data link connected to an output |
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678 parameter has been fulfilled. |
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679 |
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680 ## Workflow success and failure |
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681 |
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682 A completed step must result in one of `success`, `temporaryFailure` or |
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683 `permanentFailure` states. An implementation may choose to retry a step |
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684 execution which resulted in `temporaryFailure`. An implementation may |
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685 choose to either continue running other steps of a workflow, or terminate |
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686 immediately upon `permanentFailure`. |
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687 |
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688 * If any step of a workflow execution results in `permanentFailure`, then |
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689 the workflow status is `permanentFailure`. |
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690 |
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691 * If one or more steps result in `temporaryFailure` and all other steps |
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692 complete `success` or are not executed, then the workflow status is |
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693 `temporaryFailure`. |
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694 |
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695 * If all workflow steps are executed and complete with `success`, then the |
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696 workflow status is `success`. |
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697 |
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698 # Extensions |
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699 |
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700 [ScatterFeatureRequirement](#ScatterFeatureRequirement) and |
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701 [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are |
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702 available as standard [extensions](#Extensions_and_Metadata) to core |
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703 workflow semantics. |
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704 |
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705 fields: |
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706 - name: "class" |
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707 jsonldPredicate: |
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708 "_id": "@type" |
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709 "_type": "@vocab" |
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710 type: string |
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711 - name: steps |
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712 doc: | |
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713 The individual steps that make up the workflow. Each step is executed when all of its |
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714 input data links are fufilled. An implementation may choose to execute |
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715 the steps in a different order than listed and/or execute steps |
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716 concurrently, provided that dependencies between steps are met. |
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717 type: |
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718 - type: array |
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719 items: "#WorkflowStep" |
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720 jsonldPredicate: |
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721 mapSubject: id |
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722 |
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723 |
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724 - type: record |
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725 name: SubworkflowFeatureRequirement |
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726 extends: ProcessRequirement |
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727 doc: | |
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728 Indicates that the workflow platform must support nested workflows in |
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729 the `run` field of [WorkflowStep](#WorkflowStep). |
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|
730 fields: |
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731 - name: "class" |
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732 type: "string" |
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733 doc: "Always 'SubworkflowFeatureRequirement'" |
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734 jsonldPredicate: |
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735 "_id": "@type" |
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736 "_type": "@vocab" |
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737 |
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738 - name: ScatterFeatureRequirement |
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739 type: record |
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740 extends: ProcessRequirement |
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741 doc: | |
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742 Indicates that the workflow platform must support the `scatter` and |
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743 `scatterMethod` fields of [WorkflowStep](#WorkflowStep). |
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744 fields: |
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|
745 - name: "class" |
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|
746 type: "string" |
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747 doc: "Always 'ScatterFeatureRequirement'" |
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|
748 jsonldPredicate: |
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749 "_id": "@type" |
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|
750 "_type": "@vocab" |
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|
751 |
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|
752 - name: MultipleInputFeatureRequirement |
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|
753 type: record |
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|
754 extends: ProcessRequirement |
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|
755 doc: | |
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|
756 Indicates that the workflow platform must support multiple inbound data links |
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|
757 listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput). |
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|
758 fields: |
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|
759 - name: "class" |
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|
760 type: "string" |
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|
761 doc: "Always 'MultipleInputFeatureRequirement'" |
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|
762 jsonldPredicate: |
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|
763 "_id": "@type" |
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|
764 "_type": "@vocab" |
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|
765 |
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|
766 - type: record |
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|
767 name: StepInputExpressionRequirement |
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|
768 extends: ProcessRequirement |
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|
769 doc: | |
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|
770 Indicate that the workflow platform must support the `valueFrom` field |
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|
771 of [WorkflowStepInput](#WorkflowStepInput). |
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|
772 fields: |
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|
773 - name: "class" |
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|
774 type: "string" |
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|
775 doc: "Always 'StepInputExpressionRequirement'" |
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776 jsonldPredicate: |
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|
777 "_id": "@type" |
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|
778 "_type": "@vocab" |
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parents:
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|
779 |
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|
780 - {$import: Operation.yml} |