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annotate env/lib/python3.7/site-packages/cwltool/schemas/v1.1.0-dev1/concepts.md @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
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1 ## References to other specifications
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2
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3 **Javascript Object Notation (JSON)**: http://json.org
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4
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5 **JSON Linked Data (JSON-LD)**: http://json-ld.org
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6
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7 **YAML**: http://yaml.org
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8
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9 **Avro**: https://avro.apache.org/docs/1.8.1/spec.html
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10
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11 **Uniform Resource Identifier (URI) Generic Syntax**: https://tools.ietf.org/html/rfc3986)
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12
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13 **Internationalized Resource Identifiers (IRIs)**:
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14 https://tools.ietf.org/html/rfc3987
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15
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16 **Portable Operating System Interface (POSIX.1-2008)**: http://pubs.opengroup.org/onlinepubs/9699919799/
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17
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18 **Resource Description Framework (RDF)**: http://www.w3.org/RDF/
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19
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20 ## Scope
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21
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22 This document describes CWL syntax, execution, and object model. It
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23 is not intended to document a CWL specific implementation, however it may
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24 serve as a reference for the behavior of conforming implementations.
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25
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26 ## Terminology
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27
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28 The terminology used to describe CWL documents is defined in the
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29 Concepts section of the specification. The terms defined in the
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30 following list are used in building those definitions and in describing the
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31 actions of a CWL implementation:
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32
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33 **may**: Conforming CWL documents and CWL implementations are permitted but
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34 not required to behave as described.
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35
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36 **must**: Conforming CWL documents and CWL implementations are required to behave
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37 as described; otherwise they are in error.
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38
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39 **error**: A violation of the rules of this specification; results are
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40 undefined. Conforming implementations may detect and report an error and may
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41 recover from it.
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42
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43 **fatal error**: A violation of the rules of this specification; results are
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44 undefined. Conforming implementations must not continue to execute the current
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45 process and may report an error.
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46
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47 **at user option**: Conforming software may or must (depending on the modal verb in
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48 the sentence) behave as described; if it does, it must provide users a means to
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49 enable or disable the behavior described.
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50
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51 **deprecated**: Conforming software may implement a behavior for backwards
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52 compatibility. Portable CWL documents should not rely on deprecated behavior.
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53 Behavior marked as deprecated may be removed entirely from future revisions of
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54 the CWL specification.
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55
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56 # Data model
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57
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58 ## Data concepts
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59
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60 An **object** is a data structure equivalent to the "object" type in JSON,
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61 consisting of a unordered set of name/value pairs (referred to here as
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62 **fields**) and where the name is a string and the value is a string, number,
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63 boolean, array, or object.
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64
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65 A **document** is a file containing a serialized object, or an array of objects.
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66
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67 A **process** is a basic unit of computation which accepts input data,
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68 performs some computation, and produces output data. Examples include
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69 CommandLineTools, Workflows, and ExpressionTools.
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70
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71 An **input object** is an object describing the inputs to an invocation of
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72 a process.
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73
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74 An **output object** is an object describing the output resulting from an
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75 invocation of a process.
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76
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77 An **input schema** describes the valid format (required fields, data types)
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78 for an input object.
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79
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80 An **output schema** describes the valid format for an output object.
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81
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82 **Metadata** is information about workflows, tools, or input items.
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83
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84 ## Syntax
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85
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86 CWL documents must consist of an object or array of objects represented using
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87 JSON or YAML syntax. Upon loading, a CWL implementation must apply the
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88 preprocessing steps described in the
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89 [Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html).
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90 An implementation may formally validate the structure of a CWL document using
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91 SALAD schemas located at
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92 https://github.com/common-workflow-language/common-workflow-language/tree/master/v1.1.0-dev1
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93
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94 ### map
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95
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96 Note: This section is non-normative.
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97 > type: array<ComplexType> |
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98 > map<`key_field`, ComplexType>
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99
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100 The above syntax in the CWL specifications means there are two or more ways to write the given value.
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101
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102 Option one is a array and is the most verbose option.
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103
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104 Option one generic example:
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105 ```
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106 some_cwl_field:
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107 - key_field: a_complex_type1
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108 field2: foo
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109 field3: bar
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110 - key_field: a_complex_type2
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111 field2: foo2
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112 field3: bar2
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113 - key_field: a_complex_type3
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114 ```
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115
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116 Option one specific example using [Workflow](Workflow.html#Workflow).[inputs](Workflow.html#WorkflowInputParameter):
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117 > array<InputParameter> |
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118 > map<`id`, `type` | InputParameter>
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119
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120
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121 ```
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122 inputs:
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123 - id: workflow_input01
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124 type: string
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125 - id: workflow_input02
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126 type: File
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127 format: http://edamontology.org/format_2572
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128 ```
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129
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130 Option two is enabled by the `map<…>` syntax. Instead of an array of entries we
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131 use a mapping, where one field of the `ComplexType` (here named `key_field`)
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132 becomes the key in the map, and its value is the rest of the `ComplexType`
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133 without the key field. If all of the other fields of the `ComplexType` are
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134 optional and unneeded, then we can indicate this with an empty mapping as the
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135 value: `a_complex_type3: {}`
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136
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137 Option two generic example:
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138 ```
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139 some_cwl_field:
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140 a_complex_type1: # this was the "key_field" from above
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141 field2: foo
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142 field3: bar
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143 a_complex_type2:
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144 field2: foo2
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145 field3: bar2
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146 a_complex_type3: {} # we accept the defualt values for "field2" and "field3"
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147 ```
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148
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149 Option two specific example using [Workflow](Workflow.html#Workflow).[inputs](Workflow.html#WorkflowInputParameter):
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150 > array&lt;InputParameter&gt; |
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151 > map&lt;`id`, `type` | InputParameter&gt;
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152
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153
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154 ```
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155 inputs:
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156 workflow_input01:
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157 type: string
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158 workflow_input02:
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159 type: File
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160 format: http://edamontology.org/format_2572
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161 ```
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162
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163 Option two specific example using [SoftwareRequirement](#SoftwareRequirement).[packages](#SoftwarePackage):
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164 > array&lt;SoftwarePackage&gt; |
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165 > map&lt;`package`, `specs` | SoftwarePackage&gt;
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166
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167
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168 ```
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169 hints:
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170 SoftwareRequirement:
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171 packages:
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172 sourmash:
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173 specs: [ https://doi.org/10.21105/joss.00027 ]
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174 screed:
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175 version: [ "1.0" ]
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176 python: {}
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177 ```
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178 `
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179 Sometimes we have a third and even more compact option denoted like this:
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180 > type: array&lt;ComplexType&gt; |
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181 > map&lt;`key_field`, `field2` | ComplexType&gt;
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182
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183 For this example, if we only need the `key_field` and `field2` when specifying
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184 our `ComplexType`s (because the other fields are optional and we are fine with
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185 their default values) then we can abbreviate.
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186
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187 Option three generic example:
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188 ```
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189 some_cwl_field:
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190 a_complex_type1: foo # we accept the default value for field3
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191 a_complex_type2: foo2 # we accept the default value for field3
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192 a_complex_type3: {} # we accept the default values for "field2" and "field3"
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193 ```
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194
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195 Option three specific example using [Workflow](Workflow.html#Workflow).[inputs](Workflow.html#WorkflowInputParameter):
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196 > array&lt;InputParameter&gt; |
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197 > map&lt;`id`, `type` | InputParameter&gt;
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198
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199
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200 ```
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201 inputs:
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202 workflow_input01: string
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203 workflow_input02: File # we accept the default of no File format
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204 ```
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205
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206 Option three specific example using [SoftwareRequirement](#SoftwareRequirement).[packages](#SoftwarePackage):
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207 > array&lt;SoftwarePackage&gt; |
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208 > map&lt;`package`, `specs` | SoftwarePackage&gt;
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209
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210
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211 ```
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212 hints:
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213 SoftwareRequirement:
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214 packages:
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215 sourmash: [ https://doi.org/10.21105/joss.00027 ]
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216 python: {}
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217 ```
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218
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219
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220 What if some entries we want to mix the option 2 and 3? You can!
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221
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222 Mixed option 2 and 3 generic example:
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223 ```
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224 some_cwl_field:
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225 my_complex_type1: foo # we accept the default value for field3
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226 my_complex_type2:
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227 field2: foo2
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228 field3: bar2 # we did not accept the default value for field3
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229 # so we had to use the slightly expanded syntax
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230 my_complex_type3: {} # as before, we accept the default values for both
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231 # "field2" and "field3"
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232 ```
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233
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234 Mixed option 2 and 3 specific example using [Workflow](Workflow.html#Workflow).[inputs](Workflow.html#WorkflowInputParameter):
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235 > array&lt;InputParameter&gt; |
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236 > map&lt;`id`, `type` | InputParameter&gt;
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237
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238
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239 ```
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240 inputs:
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241 workflow_input01: string
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242 workflow_input02: # we use the longer way
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243 type: File # because we want to specify the "format" too
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244 format: http://edamontology.org/format_2572
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245 workflow_input03: {} # back to the short form as this entry
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246 # uses the default of no "type" just like the prior
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247 # examples
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248 ```
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249
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250 Mixed option 2 and 3 specific example using [SoftwareRequirement](#SoftwareRequirement).[packages](#SoftwarePackage):
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251 > array&lt;SoftwarePackage&gt; |
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252 > map&lt;`package`, `specs` | SoftwarePackage&gt;
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253
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254
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255 ```
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256 hints:
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257 SoftwareRequirement:
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258 packages:
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259 sourmash: [ https://doi.org/10.21105/joss.00027 ]
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260 screed:
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261 specs: [ https://github.com/dib-lab/screed ]
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262 version: [ "1.0" ]
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263 python: {}
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264 ```
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265
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266 Note: The `map<…>` (compact) versions are optional, the verbose option #1 is
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267 always allowed, but for presentation reasons option 3 and 2 may be preferred
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268 by human readers.
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269
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270 The normative explanation for these variations, aimed at implementors, is in the
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271 [Schema Salad specification](SchemaSalad.html#Identifier_maps).
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272
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273 ## Identifiers
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274
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275 If an object contains an `id` field, that is used to uniquely identify the
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276 object in that document. The value of the `id` field must be unique over the
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277 entire document. Identifiers may be resolved relative to either the document
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278 base and/or other identifiers following the rules are described in the
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279 [Schema Salad specification](SchemaSalad.html#Identifier_resolution).
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280
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281 An implementation may choose to only honor references to object types for
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282 which the `id` field is explicitly listed in this specification.
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283
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284 ## Document preprocessing
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285
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286 An implementation must resolve [$import](SchemaSalad.html#Import) and
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287 [$include](SchemaSalad.html#Import) directives as described in the
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288 [Schema Salad specification](SchemaSalad.html).
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289
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290 Another transformation defined in Schema salad is simplification of data type definitions.
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291 Type `<T>` ending with `?` should be transformed to `[<T>, "null"]`.
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292 Type `<T>` ending with `[]` should be transformed to `{"type": "array", "items": <T>}`
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293
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294 ## Extensions and metadata
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295
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296 Input metadata (for example, a lab sample identifier) may be represented within
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297 a tool or workflow using input parameters which are explicitly propagated to
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298 output. Future versions of this specification may define additional facilities
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299 for working with input/output metadata.
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300
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301 Implementation extensions not required for correct execution (for example,
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302 fields related to GUI presentation) and metadata about the tool or workflow
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303 itself (for example, authorship for use in citations) may be provided as
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304 additional fields on any object. Such extensions fields must use a namespace
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305 prefix listed in the `$namespaces` section of the document as described in the
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306 [Schema Salad specification](SchemaSalad.html#Explicit_context).
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307
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308 Implementation extensions which modify execution semantics must be [listed in
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309 the `requirements` field](#Requirements_and_hints).
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310
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311 # Execution model
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312
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313 ## Execution concepts
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314
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315 A **parameter** is a named symbolic input or output of process, with an
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316 associated datatype or schema. During execution, values are assigned to
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317 parameters to make the input object or output object used for concrete
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318 process invocation.
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319
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320 A **CommandLineTool** is a process characterized by the execution of a
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321 standalone, non-interactive program which is invoked on some input,
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322 produces output, and then terminates.
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323
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324 A **workflow** is a process characterized by multiple subprocess steps,
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325 where step outputs are connected to the inputs of downstream steps to
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326 form a directed acylic graph, and independent steps may run concurrently.
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327
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328 A **runtime environment** is the actual hardware and software environment when
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329 executing a command line tool. It includes, but is not limited to, the
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330 hardware architecture, hardware resources, operating system, software runtime
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331 (if applicable, such as the specific Python interpreter or the specific Java
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332 virtual machine), libraries, modules, packages, utilities, and data files
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333 required to run the tool.
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334
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335 A **workflow platform** is a specific hardware and software implementation
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336 capable of interpreting CWL documents and executing the processes specified by
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337 the document. The responsibilities of the workflow platform may include
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338 scheduling process invocation, setting up the necessary runtime environment,
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339 making input data available, invoking the tool process, and collecting output.
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340
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341 A workflow platform may choose to only implement the Command Line Tool
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342 Description part of the CWL specification.
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343
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344 It is intended that the workflow platform has broad leeway outside of this
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345 specification to optimize use of computing resources and enforce policies
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346 not covered by this specification. Some areas that are currently out of
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347 scope for CWL specification but may be handled by a specific workflow
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348 platform include:
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349
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350 * Data security and permissions
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351 * Scheduling tool invocations on remote cluster or cloud compute nodes.
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352 * Using virtual machines or operating system containers to manage the runtime
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353 (except as described in [DockerRequirement](CommandLineTool.html#DockerRequirement)).
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354 * Using remote or distributed file systems to manage input and output files.
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355 * Transforming file paths.
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356 * Determining if a process has previously been executed, and if so skipping it
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357 and reusing previous results.
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358 * Pausing, resuming or checkpointing processes or workflows.
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359
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360 Conforming CWL processes must not assume anything about the runtime
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361 environment or workflow platform unless explicitly declared though the use
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362 of [process requirements](#Requirements_and_hints).
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363
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364 ## Generic execution process
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365
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366 The generic execution sequence of a CWL process (including workflows and
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367 command line line tools) is as follows.
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368
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369 1. Load input object.
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370 1. Load, process and validate a CWL document, yielding one or more process objects.
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371 1. If there are multiple process objects (due to [`$graph`](SchemaSalad.html#Document_graph))
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372 and which process object to start with is not specified in the input object (via
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373 a [`cwl:tool`](#Executing_CWL_documents_as_scripts) entry) or by any other means
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374 (like a URL fragment) then choose the process with the `id` of "#main" or "main".
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375 1. Validate the input object against the `inputs` schema for the process.
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376 1. Validate process requirements are met.
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377 1. Perform any further setup required by the specific process type.
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378 1. Execute the process.
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379 1. Capture results of process execution into the output object.
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380 1. Validate the output object against the `outputs` schema for the process.
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381 1. Report the output object to the process caller.
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382
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383 ## Requirements and hints
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384
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385 A **process requirement** modifies the semantics or runtime
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386 environment of a process. If an implementation cannot satisfy all
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387 requirements, or a requirement is listed which is not recognized by the
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388 implementation, it is a fatal error and the implementation must not attempt
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389 to run the process, unless overridden at user option.
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390
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391 A **hint** is similar to a requirement; however, it is not an error if an
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392 implementation cannot satisfy all hints. The implementation may report a
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393 warning if a hint cannot be satisfied.
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394
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395 Optionally, implementations may allow requirements to be specified in the input
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396 object document as an array of requirements under the field name
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397 `cwl:requirements`. If implementations allow this, then such requirements
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398 should be combined with any requirements present in the corresponding Process
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399 as if they were specified there.
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400
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401 Requirements specified in a parent Workflow are inherited by step processes
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402 if they are valid for that step. If the substep is a CommandLineTool
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403 only the `InlineJavascriptRequirement`, `SchemaDefRequirement`, `DockerRequirement`,
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404 `SoftwareRequirement`, `InitialWorkDirRequirement`, `EnvVarRequirement`,
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405 `ShellCommandRequirement`, `ResourceRequirement` are valid.
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406
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407 *As good practice, it is best to have process requirements be self-contained,
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408 such that each process can run successfully by itself.*
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409
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410 If the same process requirement appears at different levels of the
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411 workflow, the most specific instance of the requirement is used, that is,
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412 an entry in `requirements` on a process implementation such as
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413 CommandLineTool will take precedence over an entry in `requirements`
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414 specified in a workflow step, and an entry in `requirements` on a workflow
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415 step takes precedence over the workflow. Entries in `hints` are resolved
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416 the same way.
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417
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418 Requirements override hints. If a process implementation provides a
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419 process requirement in `hints` which is also provided in `requirements` by
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420 an enclosing workflow or workflow step, the enclosing `requirements` takes
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421 precedence.
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422
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423 ## Parameter references
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424
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425 Parameter references are denoted by the syntax `$(...)` and may be used in any
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426 field permitting the pseudo-type `Expression`, as specified by this document.
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427 Conforming implementations must support parameter references. Parameter
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428 references use the following subset of
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429 [Javascript/ECMAScript 5.1](http://www.ecma-international.org/ecma-262/5.1/)
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430 syntax, but they are designed to not require a Javascript engine for evaluation.
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431
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432 In the following [BNF
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433 grammar](https://en.wikipedia.org/wiki/Backus%E2%80%93Naur_Form), character
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434 classes, and grammar rules are denoted in '{}', '-' denotes exclusion from a
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435 character class, '(())' denotes grouping, '|' denotes alternates, trailing
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436 '*' denotes zero or more repeats, '+' denote one or more repeats, '/' escapes
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437 these special characters, and all other characters are literal values.
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438
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439 <p>
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440 <table class="table">
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441 <tr><td>symbol:: </td><td>{Unicode alphanumeric}+</td></tr>
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442 <tr><td>singleq:: </td><td>[' (( {character - '} | \' ))* ']</td></tr>
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443 <tr><td>doubleq:: </td><td>[" (( {character - "} | \" ))* "]</td></tr>
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444 <tr><td>index:: </td><td>[ {decimal digit}+ ]</td></tr>
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445 <tr><td>segment:: </td><td>. {symbol} | {singleq} | {doubleq} | {index}</td></tr>
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446 <tr><td>parameter reference::</td><td>$( {symbol} {segment}*)</td></tr>
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447 </table>
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448 </p>
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449
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450 Use the following algorithm to resolve a parameter reference:
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451
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452 1. Match the leading symbol as the key
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453 2. Look up the key in the parameter context (described below) to get the current value.
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454 It is an error if the key is not found in the parameter context.
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455 3. If there are no subsequent segments, terminate and return current value
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456 4. Else, match the next segment
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457 5. Extract the symbol, string, or index from the segment as the key
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458 6. Look up the key in current value and assign as new current value. If
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459 the key is a symbol or string, the current value must be an object.
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460 If the key is an index, the current value must be an array or string.
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461 It is an error if the key does not match the required type, or the key is not found or out
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462 of range.
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463 7. Repeat steps 3-6
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464
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465 The root namespace is the parameter context. The following parameters must
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466 be provided:
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467
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468 * `inputs`: The input object to the current Process.
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469 * `self`: A context-specific value. The contextual values for 'self' are
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470 documented for specific fields elsewhere in this specification. If
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471 a contextual value of 'self' is not documented for a field, it
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472 must be 'null'.
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473 * `runtime`: An object containing configuration details. Specific to the
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474 process type. An implementation may provide
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475 opaque strings for any or all fields of `runtime`. These must be
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476 filled in by the platform after processing the Tool but before actual
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477 execution. Parameter references and expressions may only use the
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478 literal string value of the field and must not perform computation on
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479 the contents, except where noted otherwise.
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480
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481 If the value of a field has no leading or trailing non-whitespace
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482 characters around a parameter reference, the effective value of the field
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483 becomes the value of the referenced parameter, preserving the return type.
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484
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485 If the value of a field has non-whitespace leading or trailing characters
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486 around a parameter reference, it is subject to string interpolation. The
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487 effective value of the field is a string containing the leading characters,
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488 followed by the string value of the parameter reference, followed by the
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489 trailing characters. The string value of the parameter reference is its
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490 textual JSON representation with the following rules:
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491
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492 * Leading and trailing quotes are stripped from strings
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493 * Objects entries are sorted by key
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494
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495 Multiple parameter references may appear in a single field. This case
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496 must be treated as a string interpolation. After interpolating the first
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497 parameter reference, interpolation must be recursively applied to the
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498 trailing characters to yield the final string value.
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499
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500 ## Expressions
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501
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502 An expression is a fragment of [Javascript/ECMAScript
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503 5.1](http://www.ecma-international.org/ecma-262/5.1/) code evaluated by the
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504 workflow platform to affect the inputs, outputs, or
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505 behavior of a process. In the generic execution sequence, expressions may
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506 be evaluated during step 5 (process setup), step 6 (execute process),
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507 and/or step 7 (capture output). Expressions are distinct from regular
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508 processes in that they are intended to modify the behavior of the workflow
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509 itself rather than perform the primary work of the workflow.
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510
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511 To declare the use of expressions, the document must include the process
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512 requirement `InlineJavascriptRequirement`. Expressions may be used in any
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513 field permitting the pseudo-type `Expression`, as specified by this
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514 document.
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515
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516 Expressions are denoted by the syntax `$(...)` or `${...}`. A code
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517 fragment wrapped in the `$(...)` syntax must be evaluated as a
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518 [ECMAScript expression](http://www.ecma-international.org/ecma-262/5.1/#sec-11). A
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519 code fragment wrapped in the `${...}` syntax must be evaluated as a
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520 [ECMAScript function body](http://www.ecma-international.org/ecma-262/5.1/#sec-13)
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521 for an anonymous, zero-argument function. Expressions must return a valid JSON
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522 data type: one of null, string, number, boolean, array, object. Other return
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523 values must result in a `permanentFailure`. Implementations must permit any
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524 syntactically valid Javascript and account for nesting of parenthesis or braces
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525 and that strings that may contain parenthesis or braces when scanning for
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526 expressions.
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diff changeset
527
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528 The runtime must include any code defined in the ["expressionLib" field of
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529 InlineJavascriptRequirement](#InlineJavascriptRequirement) prior to
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diff changeset
530 executing the actual expression.
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diff changeset
531
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532 Before executing the expression, the runtime must initialize as global
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533 variables the fields of the parameter context described above.
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diff changeset
534
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535 The effective value of the field after expression evaluation follows the
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536 same rules as parameter references discussed above. Multiple expressions
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diff changeset
537 may appear in a single field.
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diff changeset
538
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539 Expressions must be evaluated in an isolated context (a "sandbox") which
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diff changeset
540 permits no side effects to leak outside the context. Expressions also must
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diff changeset
541 be evaluated in [Javascript strict mode](http://www.ecma-international.org/ecma-262/5.1/#sec-4.2.2).
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diff changeset
542
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diff changeset
543 The order in which expressions are evaluated is undefined except where
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diff changeset
544 otherwise noted in this document.
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diff changeset
545
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546 An implementation may choose to implement parameter references by
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547 evaluating as a Javascript expression. The results of evaluating
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diff changeset
548 parameter references must be identical whether implemented by Javascript
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diff changeset
549 evaluation or some other means.
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diff changeset
550
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diff changeset
551 Implementations may apply other limits, such as process isolation, timeouts,
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552 and operating system containers/jails to minimize the security risks associated
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553 with running untrusted code embedded in a CWL document.
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diff changeset
554
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diff changeset
555 Exceptions thrown from an exception must result in a `permanentFailure` of the
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diff changeset
556 process.
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diff changeset
557
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558 ## Executing CWL documents as scripts
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diff changeset
559
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560 By convention, a CWL document may begin with `#!/usr/bin/env cwl-runner`
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561 and be marked as executable (the POSIX "+x" permission bits) to enable it
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562 to be executed directly. A workflow platform may support this mode of
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563 operation; if so, it must provide `cwl-runner` as an alias for the
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diff changeset
564 platform's CWL implementation.
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diff changeset
565
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566 A CWL input object document may similarly begin with `#!/usr/bin/env
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diff changeset
567 cwl-runner` and be marked as executable. In this case, the input object
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diff changeset
568 must include the field `cwl:tool` supplying an IRI to the default CWL
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diff changeset
569 document that should be executed using the fields of the input object as
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diff changeset
570 input parameters.
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diff changeset
571
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diff changeset
572 The `cwl-runner` interface is required for conformance testing and is
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diff changeset
573 documented in [cwl-runner.cwl](cwl-runner.cwl).
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574
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575 ## Discovering CWL documents on a local filesystem
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diff changeset
576
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diff changeset
577 To discover CWL documents look in the following locations:
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diff changeset
578
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diff changeset
579 `/usr/share/commonwl/`
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diff changeset
580
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diff changeset
581 `/usr/local/share/commonwl/`
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diff changeset
582
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diff changeset
583 `$XDG_DATA_HOME/commonwl/` (usually `$HOME/.local/share/commonwl`)
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584
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diff changeset
585 `$XDG_DATA_HOME` is from the [XDG Base Directory
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diff changeset
586 Specification](http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html)