Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.2.0-dev2/CommandLineTool.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 |
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7 $graph: |
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8 |
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9 - name: CommandLineToolDoc |
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10 type: documentation |
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11 doc: |
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12 - | |
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13 # Common Workflow Language (CWL) Command Line Tool Description, v1.2.0-dev2 |
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14 |
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15 This version: |
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16 * https://w3id.org/cwl/v1.2.0-dev2/ |
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17 |
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18 Current version: |
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19 * https://w3id.org/cwl/ |
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20 - "\n\n" |
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21 - {$include: contrib.md} |
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22 - "\n\n" |
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23 - | |
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24 # Abstract |
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25 |
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26 A Command Line Tool is a non-interactive executable program that reads |
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27 some input, performs a computation, and terminates after producing some |
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28 output. Command line programs are a flexible unit of code sharing and |
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29 reuse, unfortunately the syntax and input/output semantics among command |
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30 line programs is extremely heterogeneous. A common layer for describing |
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31 the syntax and semantics of programs can reduce this incidental |
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32 complexity by providing a consistent way to connect programs together. |
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33 This specification defines the Common Workflow Language (CWL) Command |
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34 Line Tool Description, a vendor-neutral standard for describing the |
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35 syntax and input/output semantics of command line programs. |
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36 |
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37 - {$include: intro.md} |
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38 |
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39 - | |
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40 ## Introduction to the CWL Command Line Tool standard v1.2.0-dev2 |
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41 |
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42 This specification represents the latest development release from the |
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43 CWL group. Since the v1.1 release, v1.2.0-dev2 introduces the |
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44 following updates to the CWL Command Line Tool standard. |
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45 Documents should use `cwlVersion: v1.2.0-dev2` to make use of new |
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46 syntax and features introduced in v1.2.0-dev2. Existing v1.1 documents |
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47 should be trivially updatable by changing `cwlVersion`, however |
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48 CWL documents that relied on previously undefined or |
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49 underspecified behavior may have slightly different behavior in |
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50 v1.2.0-dev2. |
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51 |
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52 ## Changelog |
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53 |
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54 * `coresMin` and `coresMax` of |
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55 [ResourceRequirement](#ResourceRequirement) may now request fractional CPUs. |
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56 * (CommandLineTool)[#CommandLineTool] can now express `intent` |
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57 with an identifier for the type of computational operation. |
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58 |
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59 See also the [CWL Workflow Description, v1.2.0-dev2 changelog](Workflow.html#Changelog). |
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60 |
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61 ## Purpose |
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62 |
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63 Standalone programs are a flexible and interoperable form of code reuse. |
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64 Unlike monolithic applications, applications and analysis workflows which |
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65 are composed of multiple separate programs can be written in multiple |
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66 languages and execute concurrently on multiple hosts. However, POSIX |
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67 does not dictate computer-readable grammar or semantics for program input |
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68 and output, resulting in extremely heterogeneous command line grammar and |
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69 input/output semantics among program. This is a particular problem in |
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70 distributed computing (multi-node compute clusters) and virtualized |
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71 environments (such as Docker containers) where it is often necessary to |
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72 provision resources such as input files before executing the program. |
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73 |
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74 Often this gap is filled by hard coding program invocation and |
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75 implicitly assuming requirements will be met, or abstracting program |
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76 invocation with wrapper scripts or descriptor documents. Unfortunately, |
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77 where these approaches are application or platform specific it creates a |
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78 significant barrier to reproducibility and portability, as methods |
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79 developed for one platform must be manually ported to be used on new |
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80 platforms. Similarly it creates redundant work, as wrappers for popular |
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81 tools must be rewritten for each application or platform in use. |
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82 |
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83 The Common Workflow Language Command Line Tool Description is designed to |
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84 provide a common standard description of grammar and semantics for |
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85 invoking programs used in data-intensive fields such as Bioinformatics, |
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86 Chemistry, Physics, Astronomy, and Statistics. This specification |
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87 attempts to define a precise data and execution model for Command Line Tools that |
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88 can be implemented on a variety of computing platforms, ranging from a |
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89 single workstation to cluster, grid, cloud, and high performance |
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90 computing platforms. Details related to execution of these programs not |
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91 laid out in this specification are open to interpretation by the computing |
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92 platform implementing this specification. |
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93 |
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94 - {$include: concepts.md} |
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95 - {$include: invocation.md} |
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96 |
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97 |
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98 - type: record |
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99 name: EnvironmentDef |
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100 doc: | |
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101 Define an environment variable that will be set in the runtime environment |
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102 by the workflow platform when executing the command line tool. May be the |
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103 result of executing an expression, such as getting a parameter from input. |
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104 fields: |
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105 - name: envName |
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106 type: string |
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107 doc: The environment variable name |
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108 - name: envValue |
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109 type: [string, Expression] |
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110 doc: The environment variable value |
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111 |
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112 - type: record |
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113 name: CommandLineBinding |
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114 extends: InputBinding |
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115 docParent: "#CommandInputParameter" |
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116 doc: | |
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117 |
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118 When listed under `inputBinding` in the input schema, the term |
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119 "value" refers to the the corresponding value in the input object. For |
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120 binding objects listed in `CommandLineTool.arguments`, the term "value" |
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121 refers to the effective value after evaluating `valueFrom`. |
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122 |
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123 The binding behavior when building the command line depends on the data |
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124 type of the value. If there is a mismatch between the type described by |
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125 the input schema and the effective value, such as resulting from an |
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126 expression evaluation, an implementation must use the data type of the |
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127 effective value. |
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128 |
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129 - **string**: Add `prefix` and the string to the command line. |
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130 |
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131 - **number**: Add `prefix` and decimal representation to command line. |
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132 |
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133 - **boolean**: If true, add `prefix` to the command line. If false, add |
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134 nothing. |
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135 |
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136 - **File**: Add `prefix` and the value of |
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137 [`File.path`](#File) to the command line. |
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138 |
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139 - **Directory**: Add `prefix` and the value of |
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140 [`Directory.path`](#Directory) to the command line. |
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141 |
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142 - **array**: If `itemSeparator` is specified, add `prefix` and the join |
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143 the array into a single string with `itemSeparator` separating the |
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144 items. Otherwise first add `prefix`, then recursively process |
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145 individual elements. |
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146 If the array is empty, it does not add anything to command line. |
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147 |
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148 - **object**: Add `prefix` only, and recursively add object fields for |
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149 which `inputBinding` is specified. |
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150 |
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151 - **null**: Add nothing. |
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152 |
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153 fields: |
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154 - name: position |
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155 type: [ "null", int, Expression ] |
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156 doc: | |
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157 The sorting key. Default position is 0. If the inputBinding is |
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158 associated with an input parameter, then the value of `self` in the |
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159 expression will be the value of the input parameter. Input parameter |
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160 defaults (as specified by the `InputParameter.default` field) must be |
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161 applied before evaluating the expression. Expressions must return a |
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162 single value of type int or a null. |
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163 - name: prefix |
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164 type: string? |
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165 doc: "Command line prefix to add before the value." |
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166 - name: separate |
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167 type: boolean? |
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168 default: true |
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169 doc: | |
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170 If true (default), then the prefix and value must be added as separate |
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171 command line arguments; if false, prefix and value must be concatenated |
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172 into a single command line argument. |
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173 - name: itemSeparator |
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174 type: string? |
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175 doc: | |
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176 Join the array elements into a single string with the elements |
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177 separated by by `itemSeparator`. |
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178 - name: valueFrom |
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179 type: |
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180 - "null" |
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181 - string |
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182 - Expression |
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183 jsonldPredicate: "cwl:valueFrom" |
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184 doc: | |
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185 If `valueFrom` is a constant string value, use this as the value and |
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186 apply the binding rules above. |
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187 |
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188 If `valueFrom` is an expression, evaluate the expression to yield the |
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189 actual value to use to build the command line and apply the binding |
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190 rules above. If the inputBinding is associated with an input |
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191 parameter, the value of `self` in the expression will be the value of |
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192 the input parameter. Input parameter defaults (as specified by the |
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193 `InputParameter.default` field) must be applied before evaluating the |
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194 expression. |
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195 |
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196 If the value of the associated input parameter is `null`, `valueFrom` is |
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197 not evaluated and nothing is added to the command line. |
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198 |
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199 When a binding is part of the `CommandLineTool.arguments` field, |
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200 the `valueFrom` field is required. |
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201 |
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202 - name: shellQuote |
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203 type: boolean? |
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204 default: true |
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205 doc: | |
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206 If `ShellCommandRequirement` is in the requirements for the current command, |
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207 this controls whether the value is quoted on the command line (default is true). |
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208 Use `shellQuote: false` to inject metacharacters for operations such as pipes. |
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209 |
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210 If `shellQuote` is true or not provided, the implementation must not |
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211 permit interpretation of any shell metacharacters or directives. |
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212 |
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213 |
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214 - type: record |
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215 name: CommandOutputBinding |
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216 extends: LoadContents |
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217 doc: | |
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218 Describes how to generate an output parameter based on the files produced |
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219 by a CommandLineTool. |
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220 |
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221 The output parameter value is generated by applying these operations in the |
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222 following order: |
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223 |
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224 - glob |
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225 - loadContents |
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226 - outputEval |
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227 - secondaryFiles |
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228 fields: |
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229 - name: glob |
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230 type: |
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231 - "null" |
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232 - string |
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233 - Expression |
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234 - type: array |
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235 items: string |
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236 doc: | |
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237 Find files or directories relative to the output directory, using POSIX |
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238 glob(3) pathname matching. If an array is provided, find files or |
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239 directories that match any pattern in the array. If an expression is |
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240 provided, the expression must return a string or an array of strings, |
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241 which will then be evaluated as one or more glob patterns. Must only |
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242 match and return files/directories which actually exist. |
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243 |
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244 If the value of glob is a relative path pattern (does not |
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245 begin with a slash '/') then it is resolved relative to the |
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246 output directory. If the value of the glob is an absolute |
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247 path pattern (it does begin with a slash '/') then it must |
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248 refer to a path within the output directory. It is an error |
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249 if any glob resolves to a path outside the output directory. |
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250 Specifically this means globs that resolve to paths outside the output |
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251 directory are illegal. |
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252 |
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253 A glob may match a path within the output directory which is |
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254 actually a symlink to another file. In this case, the |
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255 expected behavior is for the resulting File/Directory object to take the |
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256 `basename` (and corresponding `nameroot` and `nameext`) of the |
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257 symlink. The `location` of the File/Directory is implementation |
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258 dependent, but logically the File/Directory should have the same content |
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259 as the symlink target. Platforms may stage output files/directories to |
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260 cloud storage that lack the concept of a symlink. In |
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261 this case file content and directories may be duplicated, or (to avoid |
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262 duplication) the File/Directory `location` may refer to the symlink |
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263 target. |
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264 |
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265 It is an error if a symlink in the output directory (or any |
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266 symlink in a chain of links) refers to any file or directory |
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267 that is not under an input or output directory. |
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268 |
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269 Implementations may shut down a container before globbing |
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270 output, so globs and expressions must not assume access to the |
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271 container filesystem except for declared input and output. |
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272 |
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273 - name: outputEval |
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274 type: Expression? |
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275 doc: | |
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276 Evaluate an expression to generate the output value. If |
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277 `glob` was specified, the value of `self` must be an array |
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278 containing file objects that were matched. If no files were |
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279 matched, `self` must be a zero length array; if a single file |
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280 was matched, the value of `self` is an array of a single |
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281 element. Additionally, if `loadContents` is `true`, the File |
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282 objects must include up to the first 64 KiB of file contents |
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283 in the `contents` field. The exit code of the process is |
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284 available in the expression as `runtime.exitCode`. |
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285 |
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286 - name: CommandLineBindable |
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287 type: record |
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288 fields: |
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289 inputBinding: |
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290 type: CommandLineBinding? |
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291 jsonldPredicate: "cwl:inputBinding" |
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292 doc: Describes how to turn this object into command line arguments. |
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293 |
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294 - name: CommandInputRecordField |
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295 type: record |
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296 extends: [InputRecordField, CommandLineBindable] |
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297 specialize: |
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298 - specializeFrom: InputRecordSchema |
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299 specializeTo: CommandInputRecordSchema |
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300 - specializeFrom: InputEnumSchema |
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301 specializeTo: CommandInputEnumSchema |
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302 - specializeFrom: InputArraySchema |
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303 specializeTo: CommandInputArraySchema |
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304 - specializeFrom: InputBinding |
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305 specializeTo: CommandLineBinding |
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306 |
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307 |
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308 - name: CommandInputRecordSchema |
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309 type: record |
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310 extends: [InputRecordSchema, CommandInputSchema, CommandLineBindable] |
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311 specialize: |
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312 - specializeFrom: InputRecordField |
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313 specializeTo: CommandInputRecordField |
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314 - specializeFrom: InputBinding |
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315 specializeTo: CommandLineBinding |
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316 |
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317 |
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318 - name: CommandInputEnumSchema |
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319 type: record |
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320 extends: [InputEnumSchema, CommandInputSchema, CommandLineBindable] |
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321 specialize: |
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322 - specializeFrom: InputBinding |
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323 specializeTo: CommandLineBinding |
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324 |
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325 |
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326 - name: CommandInputArraySchema |
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327 type: record |
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328 extends: [InputArraySchema, CommandInputSchema, CommandLineBindable] |
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329 specialize: |
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330 - specializeFrom: InputRecordSchema |
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331 specializeTo: CommandInputRecordSchema |
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332 - specializeFrom: InputEnumSchema |
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333 specializeTo: CommandInputEnumSchema |
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334 - specializeFrom: InputArraySchema |
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335 specializeTo: CommandInputArraySchema |
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336 - specializeFrom: InputBinding |
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337 specializeTo: CommandLineBinding |
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|
338 |
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|
339 |
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|
340 - name: CommandOutputRecordField |
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341 type: record |
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|
342 extends: OutputRecordField |
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|
343 specialize: |
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|
344 - specializeFrom: OutputRecordSchema |
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|
345 specializeTo: CommandOutputRecordSchema |
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|
346 - specializeFrom: OutputEnumSchema |
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|
347 specializeTo: CommandOutputEnumSchema |
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348 - specializeFrom: OutputArraySchema |
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349 specializeTo: CommandOutputArraySchema |
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|
350 fields: |
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351 - name: outputBinding |
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352 type: CommandOutputBinding? |
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|
353 jsonldPredicate: "cwl:outputBinding" |
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|
354 doc: | |
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|
355 Describes how to generate this output object based on the files |
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356 produced by a CommandLineTool |
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|
357 |
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|
358 |
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|
359 - name: CommandOutputRecordSchema |
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360 type: record |
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361 extends: OutputRecordSchema |
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|
362 specialize: |
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|
363 - specializeFrom: OutputRecordField |
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364 specializeTo: CommandOutputRecordField |
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|
365 |
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|
366 |
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367 - name: CommandOutputEnumSchema |
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368 type: record |
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369 extends: OutputEnumSchema |
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|
370 specialize: |
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|
371 - specializeFrom: OutputRecordSchema |
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372 specializeTo: CommandOutputRecordSchema |
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373 - specializeFrom: OutputEnumSchema |
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374 specializeTo: CommandOutputEnumSchema |
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375 - specializeFrom: OutputArraySchema |
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376 specializeTo: CommandOutputArraySchema |
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|
377 |
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|
378 |
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379 - name: CommandOutputArraySchema |
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380 type: record |
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381 extends: OutputArraySchema |
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|
382 specialize: |
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|
383 - specializeFrom: OutputRecordSchema |
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384 specializeTo: CommandOutputRecordSchema |
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385 - specializeFrom: OutputEnumSchema |
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386 specializeTo: CommandOutputEnumSchema |
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387 - specializeFrom: OutputArraySchema |
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388 specializeTo: CommandOutputArraySchema |
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|
389 |
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|
390 |
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|
391 - type: record |
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392 name: CommandInputParameter |
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393 extends: InputParameter |
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394 doc: An input parameter for a CommandLineTool. |
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|
395 fields: |
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396 - name: type |
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397 type: |
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|
398 - CWLType |
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399 - stdin |
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400 - CommandInputRecordSchema |
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|
401 - CommandInputEnumSchema |
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|
402 - CommandInputArraySchema |
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|
403 - string |
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404 - type: array |
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|
405 items: |
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|
406 - CWLType |
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|
407 - CommandInputRecordSchema |
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|
408 - CommandInputEnumSchema |
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409 - CommandInputArraySchema |
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|
410 - string |
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|
411 jsonldPredicate: |
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|
412 "_id": "sld:type" |
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|
413 "_type": "@vocab" |
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|
414 refScope: 2 |
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|
415 typeDSL: True |
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|
416 doc: | |
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417 Specify valid types of data that may be assigned to this parameter. |
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418 - name: inputBinding |
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419 type: CommandLineBinding? |
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420 doc: | |
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421 Describes how to turns the input parameters of a process into |
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|
422 command line arguments. |
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423 jsonldPredicate: "cwl:inputBinding" |
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424 |
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425 - type: record |
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426 name: CommandOutputParameter |
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427 extends: OutputParameter |
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428 doc: An output parameter for a CommandLineTool. |
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|
429 fields: |
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430 - name: type |
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431 type: |
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432 - CWLType |
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433 - stdout |
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434 - stderr |
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435 - CommandOutputRecordSchema |
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436 - CommandOutputEnumSchema |
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437 - CommandOutputArraySchema |
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|
438 - string |
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439 - type: array |
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|
440 items: |
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441 - CWLType |
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442 - CommandOutputRecordSchema |
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443 - CommandOutputEnumSchema |
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444 - CommandOutputArraySchema |
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445 - string |
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446 jsonldPredicate: |
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447 "_id": "sld:type" |
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448 "_type": "@vocab" |
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449 refScope: 2 |
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450 typeDSL: True |
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451 doc: | |
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452 Specify valid types of data that may be assigned to this parameter. |
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453 - name: outputBinding |
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454 type: CommandOutputBinding? |
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455 jsonldPredicate: "cwl:outputBinding" |
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changeset
|
456 doc: Describes how to generate this output object based on the files |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
457 produced by a CommandLineTool |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
458 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
459 - name: stdin |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
460 type: enum |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
461 symbols: [ "cwl:stdin" ] |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
462 docParent: "#CommandOutputParameter" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
463 doc: | |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
464 Only valid as a `type` for a `CommandLineTool` input with no |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
465 `inputBinding` set. `stdin` must not be specified at the `CommandLineTool` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
466 level. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
467 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
468 The following |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
469 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
470 inputs: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
471 an_input_name: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
472 type: stdin |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
473 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
474 is equivalent to |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
475 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
476 inputs: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
477 an_input_name: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
478 type: File |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
479 streamable: true |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
480 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
481 stdin: ${inputs.an_input_name.path} |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
482 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
483 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
484 - name: stdout |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
485 type: enum |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
486 symbols: [ "cwl:stdout" ] |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
487 docParent: "#CommandOutputParameter" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
488 doc: | |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
489 Only valid as a `type` for a `CommandLineTool` output with no |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
490 `outputBinding` set. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
491 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
492 The following |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
493 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
494 outputs: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
495 an_output_name: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
496 type: stdout |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
497 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
498 stdout: a_stdout_file |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
499 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
500 is equivalent to |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
501 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
502 outputs: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
503 an_output_name: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
504 type: File |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
505 streamable: true |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
506 outputBinding: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
507 glob: a_stdout_file |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
508 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
509 stdout: a_stdout_file |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
510 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
511 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
512 If there is no `stdout` name provided, a random filename will be created. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
513 For example, the following |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
514 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
515 outputs: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
516 an_output_name: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
517 type: stdout |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
518 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
519 is equivalent to |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
520 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
521 outputs: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
522 an_output_name: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
523 type: File |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
524 streamable: true |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
525 outputBinding: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
526 glob: random_stdout_filenameABCDEFG |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
527 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
528 stdout: random_stdout_filenameABCDEFG |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
529 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
530 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
531 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
532 - name: stderr |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
533 type: enum |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
534 symbols: [ "cwl:stderr" ] |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
535 docParent: "#CommandOutputParameter" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
536 doc: | |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
537 Only valid as a `type` for a `CommandLineTool` output with no |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
538 `outputBinding` set. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
539 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
540 The following |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
541 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
542 outputs: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
543 an_output_name: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
544 type: stderr |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
545 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
546 stderr: a_stderr_file |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
547 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
548 is equivalent to |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
549 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
550 outputs: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
551 an_output_name: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
552 type: File |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
553 streamable: true |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
554 outputBinding: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
555 glob: a_stderr_file |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
556 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
557 stderr: a_stderr_file |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
558 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
559 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
560 If there is no `stderr` name provided, a random filename will be created. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
561 For example, the following |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
562 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
563 outputs: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
564 an_output_name: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
565 type: stderr |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
566 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
567 is equivalent to |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
568 ``` |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
569 outputs: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
570 an_output_name: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
571 type: File |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
572 streamable: true |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
573 outputBinding: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
574 glob: random_stderr_filenameABCDEFG |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
575 |
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576 stderr: random_stderr_filenameABCDEFG |
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577 ``` |
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578 |
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579 |
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580 - type: record |
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581 name: CommandLineTool |
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582 extends: Process |
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583 documentRoot: true |
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584 specialize: |
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585 - specializeFrom: InputParameter |
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586 specializeTo: CommandInputParameter |
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587 - specializeFrom: OutputParameter |
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588 specializeTo: CommandOutputParameter |
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589 doc: | |
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590 This defines the schema of the CWL Command Line Tool Description document. |
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591 |
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592 fields: |
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593 - name: class |
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594 jsonldPredicate: |
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595 "_id": "@type" |
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596 "_type": "@vocab" |
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597 type: string |
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598 - name: baseCommand |
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599 doc: | |
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600 Specifies the program to execute. If an array, the first element of |
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601 the array is the command to execute, and subsequent elements are |
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602 mandatory command line arguments. The elements in `baseCommand` must |
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603 appear before any command line bindings from `inputBinding` or |
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604 `arguments`. |
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605 |
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606 If `baseCommand` is not provided or is an empty array, the first |
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607 element of the command line produced after processing `inputBinding` or |
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608 `arguments` must be used as the program to execute. |
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609 |
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610 If the program includes a path separator character it must |
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611 be an absolute path, otherwise it is an error. If the program does not |
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612 include a path separator, search the `$PATH` variable in the runtime |
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613 environment of the workflow runner find the absolute path of the |
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614 executable. |
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615 type: |
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616 - string? |
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617 - string[]? |
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618 jsonldPredicate: |
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619 "_id": "cwl:baseCommand" |
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620 "_container": "@list" |
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621 - name: arguments |
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622 doc: | |
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623 Command line bindings which are not directly associated with input |
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624 parameters. If the value is a string, it is used as a string literal |
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625 argument. If it is an Expression, the result of the evaluation is used |
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626 as an argument. |
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627 type: |
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628 - "null" |
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629 - type: array |
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630 items: [string, Expression, CommandLineBinding] |
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631 jsonldPredicate: |
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632 "_id": "cwl:arguments" |
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633 "_container": "@list" |
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634 - name: stdin |
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635 type: ["null", string, Expression] |
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636 jsonldPredicate: "https://w3id.org/cwl/cwl#stdin" |
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637 doc: | |
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638 A path to a file whose contents must be piped into the command's |
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639 standard input stream. |
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640 - name: stderr |
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641 type: ["null", string, Expression] |
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642 jsonldPredicate: "https://w3id.org/cwl/cwl#stderr" |
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643 doc: | |
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644 Capture the command's standard error stream to a file written to |
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645 the designated output directory. |
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646 |
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647 If `stderr` is a string, it specifies the file name to use. |
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648 |
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649 If `stderr` is an expression, the expression is evaluated and must |
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650 return a string with the file name to use to capture stderr. If the |
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651 return value is not a string, or the resulting path contains illegal |
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652 characters (such as the path separator `/`) it is an error. |
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653 - name: stdout |
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654 type: ["null", string, Expression] |
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655 jsonldPredicate: "https://w3id.org/cwl/cwl#stdout" |
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656 doc: | |
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657 Capture the command's standard output stream to a file written to |
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658 the designated output directory. |
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659 |
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660 If `stdout` is a string, it specifies the file name to use. |
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661 |
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662 If `stdout` is an expression, the expression is evaluated and must |
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663 return a string with the file name to use to capture stdout. If the |
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664 return value is not a string, or the resulting path contains illegal |
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665 characters (such as the path separator `/`) it is an error. |
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666 - name: successCodes |
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667 type: int[]? |
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668 doc: | |
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669 Exit codes that indicate the process completed successfully. |
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670 |
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671 - name: temporaryFailCodes |
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672 type: int[]? |
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673 doc: | |
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674 Exit codes that indicate the process failed due to a possibly |
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675 temporary condition, where executing the process with the same |
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676 runtime environment and inputs may produce different results. |
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677 |
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678 - name: permanentFailCodes |
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679 type: int[]? |
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680 doc: |
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681 Exit codes that indicate the process failed due to a permanent logic |
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682 error, where executing the process with the same runtime environment and |
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683 same inputs is expected to always fail. |
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684 |
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685 |
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686 - type: record |
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687 name: DockerRequirement |
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688 extends: ProcessRequirement |
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689 doc: | |
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690 Indicates that a workflow component should be run in a |
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691 [Docker](http://docker.com) or Docker-compatible (such as |
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692 [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and |
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693 specifies how to fetch or build the image. |
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694 |
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695 If a CommandLineTool lists `DockerRequirement` under |
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696 `hints` (or `requirements`), it may (or must) be run in the specified Docker |
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697 container. |
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698 |
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699 The platform must first acquire or install the correct Docker image as |
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700 specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`. |
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701 |
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702 The platform must execute the tool in the container using `docker run` with |
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703 the appropriate Docker image and tool command line. |
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704 |
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705 The workflow platform may provide input files and the designated output |
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706 directory through the use of volume bind mounts. The platform should rewrite |
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707 file paths in the input object to correspond to the Docker bind mounted |
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708 locations. That is, the platform should rewrite values in the parameter context |
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709 such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths |
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710 within the container. The platform must ensure that `runtime.outdir` and |
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711 `runtime.tmpdir` are distinct directories. |
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712 |
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713 When running a tool contained in Docker, the workflow platform must not |
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714 assume anything about the contents of the Docker container, such as the |
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715 presence or absence of specific software, except to assume that the |
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716 generated command line represents a valid command within the runtime |
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717 environment of the container. |
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718 |
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719 A container image may specify an |
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720 [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint) |
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721 and/or |
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722 [CMD](https://docs.docker.com/engine/reference/builder/#cmd). |
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723 Command line arguments will be appended after all elements of |
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724 ENTRYPOINT, and will override all elements specified using CMD (in |
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725 other words, CMD is only used when the CommandLineTool definition |
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726 produces an empty command line). |
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727 |
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728 Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility |
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729 concerns of the implicit hidden execution point (For further discussion, see |
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730 [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable |
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731 CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. |
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732 CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the |
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733 `requirements` section. |
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734 |
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735 ## Interaction with other requirements |
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736 |
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737 If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a |
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738 DockerRequirement, the environment variables must be provided to Docker |
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739 using `--env` or `--env-file` and interact with the container's preexisting |
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740 environment as defined by Docker. |
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741 |
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742 fields: |
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743 - name: class |
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744 type: string |
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745 doc: "Always 'DockerRequirement'" |
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746 jsonldPredicate: |
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747 "_id": "@type" |
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748 "_type": "@vocab" |
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749 - name: dockerPull |
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750 type: string? |
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751 doc: | |
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752 Specify a Docker image to retrieve using `docker pull`. Can contain the |
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753 immutable digest to ensure an exact container is used: |
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754 `dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2` |
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755 - name: dockerLoad |
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756 type: string? |
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757 doc: "Specify a HTTP URL from which to download a Docker image using `docker load`." |
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758 - name: dockerFile |
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759 type: string? |
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760 doc: "Supply the contents of a Dockerfile which will be built using `docker build`." |
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761 - name: dockerImport |
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762 type: string? |
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763 doc: "Provide HTTP URL to download and gunzip a Docker images using `docker import." |
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764 - name: dockerImageId |
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765 type: string? |
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|
766 doc: | |
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767 The image id that will be used for `docker run`. May be a |
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768 human-readable image name or the image identifier hash. May be skipped |
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769 if `dockerPull` is specified, in which case the `dockerPull` image id |
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770 must be used. |
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771 - name: dockerOutputDirectory |
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772 type: string? |
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773 doc: | |
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774 Set the designated output directory to a specific location inside the |
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775 Docker container. |
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776 |
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777 |
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778 - type: record |
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779 name: SoftwareRequirement |
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780 extends: ProcessRequirement |
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781 doc: | |
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782 A list of software packages that should be configured in the environment of |
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783 the defined process. |
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784 fields: |
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785 - name: class |
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|
786 type: string |
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|
787 doc: "Always 'SoftwareRequirement'" |
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788 jsonldPredicate: |
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789 "_id": "@type" |
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790 "_type": "@vocab" |
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791 - name: packages |
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792 type: SoftwarePackage[] |
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793 doc: "The list of software to be configured." |
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794 jsonldPredicate: |
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795 mapSubject: package |
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796 mapPredicate: specs |
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797 |
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798 - name: SoftwarePackage |
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799 type: record |
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800 fields: |
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801 - name: package |
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802 type: string |
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803 doc: | |
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804 The name of the software to be made available. If the name is |
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805 common, inconsistent, or otherwise ambiguous it should be combined with |
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806 one or more identifiers in the `specs` field. |
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807 - name: version |
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808 type: string[]? |
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809 doc: | |
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810 The (optional) versions of the software that are known to be |
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811 compatible. |
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812 - name: specs |
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813 type: string[]? |
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814 jsonldPredicate: {_type: "@id", noLinkCheck: true} |
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815 doc: | |
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816 One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s |
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817 identifying resources for installing or enabling the software named in |
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818 the `package` field. Implementations may provide resolvers which map |
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819 these software identifer IRIs to some configuration action; or they can |
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820 use only the name from the `package` field on a best effort basis. |
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821 |
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822 For example, the IRI https://packages.debian.org/bowtie could |
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823 be resolved with `apt-get install bowtie`. The IRI |
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824 https://anaconda.org/bioconda/bowtie could be resolved with `conda |
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825 install -c bioconda bowtie`. |
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826 |
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827 IRIs can also be system independent and used to map to a specific |
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828 software installation or selection mechanism. |
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829 Using [RRID](https://www.identifiers.org/rrid/) as an example: |
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830 https://identifiers.org/rrid/RRID:SCR_005476 |
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831 could be fulfilled using the above mentioned Debian or bioconda |
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832 package, a local installation managed by [Environement Modules](http://modules.sourceforge.net/), |
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833 or any other mechanism the platform chooses. IRIs can also be from |
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834 identifer sources that are discipline specific yet still system |
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835 independent. As an example, the equivalent [ELIXIR Tools and Data |
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836 Service Registry](https://bio.tools) IRI to the previous RRID example is |
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837 https://bio.tools/tool/bowtie2/version/2.2.8. |
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838 If supported by a given registry, implementations are encouraged to |
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839 query these system independent sofware identifier IRIs directly for |
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840 links to packaging systems. |
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841 |
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842 A site specific IRI can be listed as well. For example, an academic |
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843 computing cluster using Environement Modules could list the IRI |
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844 `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that |
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845 `module load bowtie-tbb/1.1.2` should be executed to make available |
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846 `bowtie` version 1.1.2 compiled with the TBB library prior to running |
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847 the accompanying Workflow or CommandLineTool. Note that the example IRI |
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848 is specific to a particular institution and computing environment as |
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849 the Environment Modules system does not have a common namespace or |
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850 standardized naming convention. |
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851 |
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852 This last example is the least portable and should only be used if |
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853 mechanisms based off of the `package` field or more generic IRIs are |
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854 unavailable or unsuitable. While harmless to other sites, site specific |
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855 software IRIs should be left out of shared CWL descriptions to avoid |
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856 clutter. |
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857 |
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858 - name: Dirent |
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859 type: record |
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860 doc: | |
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861 Define a file or subdirectory that must be placed in the designated output |
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862 directory prior to executing the command line tool. May be the result of |
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863 executing an expression, such as building a configuration file from a |
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864 template. |
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865 fields: |
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866 - name: entryname |
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867 type: ["null", string, Expression] |
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868 jsonldPredicate: |
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869 _id: cwl:entryname |
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870 doc: | |
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871 The name of the file or subdirectory to create in the output directory. |
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872 If `entry` is a File or Directory, the `entryname` field overrides the value |
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873 of `basename` of the File or Directory object. Optional. |
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874 - name: entry |
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875 type: [string, Expression] |
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876 jsonldPredicate: |
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877 _id: cwl:entry |
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878 doc: | |
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879 If the value is a string literal or an expression which evaluates to a |
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880 string, a new file must be created with the string as the file contents. |
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881 |
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882 If the value is an expression that evaluates to a `File` or `Directory` |
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883 object, this indicates the referenced file or directory should be added |
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884 to the designated output directory prior to executing the tool. |
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885 |
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886 If the value is an expression that evaluates to an array of `File` or |
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887 `Directory` objects, this indicates the referenced files or directories |
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888 should be added to the designated output directory prior to executing |
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889 the tool, with ignoring the value in `entryname`. |
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890 |
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891 If the value is an expression that evaluates to a `Dirent` object, this |
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892 indicates that the File or Directory in `entry` should be added to the |
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893 designated output directory with the name in `entryname`. |
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894 |
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895 If the value is an expression that evaluates to `null`, nothing is added |
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896 to the designated output directory from this entry. |
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897 |
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898 If `writable` is false, the file may be made available using a bind |
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899 mount or file system link to avoid unnecessary copying of the input |
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900 file. |
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901 - name: writable |
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902 type: boolean? |
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903 default: false |
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904 doc: | |
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905 If true, the file or directory must be writable by the tool. Changes |
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906 to the file or directory must be isolated and not visible by any other |
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907 CommandLineTool process. This may be implemented by making a copy of |
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908 the original file or directory. Default false (files and directories |
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909 read-only by default). |
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910 |
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|
911 A directory marked as `writable: true` implies that all files and |
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|
912 subdirectories are recursively writable as well. |
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|
913 |
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|
914 |
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|
915 - name: InitialWorkDirRequirement |
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|
916 type: record |
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|
917 extends: ProcessRequirement |
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|
918 doc: |
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919 Define a list of files and subdirectories that must be created by the |
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920 workflow platform in the designated output directory prior to executing the |
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|
921 command line tool. |
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|
922 fields: |
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923 - name: class |
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|
924 type: string |
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|
925 doc: InitialWorkDirRequirement |
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926 jsonldPredicate: |
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|
927 "_id": "@type" |
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|
928 "_type": "@vocab" |
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929 - name: listing |
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|
930 type: |
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931 - type: array |
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932 items: |
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|
933 - "null" |
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|
934 - File |
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935 - type: array |
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936 items: |
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|
937 - File |
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938 - Directory |
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939 - Directory |
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|
940 - Dirent |
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|
941 - Expression |
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|
942 - Expression |
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943 jsonldPredicate: |
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|
944 _id: "cwl:listing" |
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945 doc: | |
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946 The list of files or subdirectories that must be placed in the |
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947 designated output directory prior to executing the command line tool. |
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|
948 |
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949 May be an expression. If so, the expression return value must validate as |
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|
950 `{type: array, items: ["null", File, Directory, Dirent, {type: array, items: [File, Directory]}]}`. |
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|
951 |
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|
952 Files or Directories which are listed in the input parameters and |
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|
953 appear in the `InitialWorkDirRequirement` listing must have their |
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|
954 `path` set to their staged location in the designated output directory. |
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955 If the same File or Directory appears more than once in the |
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956 `InitialWorkDirRequirement` listing, the implementation must choose |
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|
957 exactly one value for `path`; how this value is chosen is undefined. |
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958 |
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|
959 |
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960 - name: EnvVarRequirement |
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961 type: record |
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962 extends: ProcessRequirement |
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963 doc: | |
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964 Define a list of environment variables which will be set in the |
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965 execution environment of the tool. See `EnvironmentDef` for details. |
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966 fields: |
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967 - name: class |
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968 type: string |
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969 doc: "Always 'EnvVarRequirement'" |
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970 jsonldPredicate: |
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971 "_id": "@type" |
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972 "_type": "@vocab" |
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973 - name: envDef |
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974 type: EnvironmentDef[] |
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975 doc: The list of environment variables. |
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976 jsonldPredicate: |
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977 mapSubject: envName |
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978 mapPredicate: envValue |
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979 |
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|
980 |
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981 - type: record |
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982 name: ShellCommandRequirement |
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983 extends: ProcessRequirement |
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984 doc: | |
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985 Modify the behavior of CommandLineTool to generate a single string |
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986 containing a shell command line. Each item in the argument list must be |
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987 joined into a string separated by single spaces and quoted to prevent |
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|
988 intepretation by the shell, unless `CommandLineBinding` for that argument |
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989 contains `shellQuote: false`. If `shellQuote: false` is specified, the |
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990 argument is joined into the command string without quoting, which allows |
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991 the use of shell metacharacters such as `|` for pipes. |
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|
992 fields: |
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993 - name: class |
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994 type: string |
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995 doc: "Always 'ShellCommandRequirement'" |
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996 jsonldPredicate: |
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997 "_id": "@type" |
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|
998 "_type": "@vocab" |
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999 |
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1000 |
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1001 - type: record |
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1002 name: ResourceRequirement |
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1003 extends: ProcessRequirement |
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1004 doc: | |
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1005 Specify basic hardware resource requirements. |
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1006 |
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1007 "min" is the minimum amount of a resource that must be reserved to schedule |
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1008 a job. If "min" cannot be satisfied, the job should not be run. |
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1009 |
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1010 "max" is the maximum amount of a resource that the job shall be permitted |
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1011 to use. If a node has sufficient resources, multiple jobs may be scheduled |
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1012 on a single node provided each job's "max" resource requirements are |
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1013 met. If a job attempts to exceed its "max" resource allocation, an |
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1014 implementation may deny additional resources, which may result in job |
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1015 failure. |
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1016 |
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1017 If "min" is specified but "max" is not, then "max" == "min" |
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1018 If "max" is specified by "min" is not, then "min" == "max". |
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1019 |
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1020 It is an error if max < min. |
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1021 |
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1022 It is an error if the value of any of these fields is negative. |
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1023 |
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1024 If neither "min" nor "max" is specified for a resource, use the default values below. |
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1025 |
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1026 fields: |
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1027 - name: class |
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1028 type: string |
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1029 doc: "Always 'ResourceRequirement'" |
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1030 jsonldPredicate: |
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1031 "_id": "@type" |
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1032 "_type": "@vocab" |
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1033 - name: coresMin |
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1034 type: ["null", long, float, Expression] |
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1035 doc: | |
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1036 Minimum reserved number of CPU cores (default is 1). |
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1037 |
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1038 May be a fractional value to indicate to a scheduling |
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1039 algorithm that one core can be allocated to multiple |
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1040 jobs. For example, a value of 0.25 indicates that up to 4 |
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1041 jobs may run in parallel on 1 core. A value of 1.25 means |
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1042 that up to 3 jobs can run on a 4 core system (4/1.25 ≈ 3). |
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1043 |
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1044 Processes can only share a core allocation if the sum of each |
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1045 of their `ramMax`, `tmpdirMax`, and `outdirMax` requests also |
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1046 do not exceed the capacity of the node. |
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1047 |
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1048 Processes sharing a core must have the same level of isolation |
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1049 (typically a container or VM) that they would normally. |
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1050 |
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1051 The reported number of CPU cores reserved for the process, |
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1052 which is available to expressions on the CommandLineTool as |
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1053 `runtime.cores`, must be a non-zero integer, and may be |
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1054 calculated by rounding up the cores request to the next whole |
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1055 number. |
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1056 |
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1057 Scheduling systems may allocate fractional CPU resources by |
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1058 setting quotas or scheduling weights. Scheduling systems that |
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1059 do not support fractional CPUs may round up the request to the |
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1060 next whole number. |
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1061 |
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1062 - name: coresMax |
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1063 type: ["null", long, float, Expression] |
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1064 doc: | |
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1065 Maximum reserved number of CPU cores. |
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1066 |
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1067 See `coresMin` for discussion about fractional CPU requests. |
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1068 |
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1069 - name: ramMin |
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1070 type: ["null", long, Expression] |
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1071 doc: Minimum reserved RAM in mebibytes (2**20) (default is 256) |
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1072 |
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1073 - name: ramMax |
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1074 type: ["null", long, Expression] |
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1075 doc: Maximum reserved RAM in mebibytes (2**20) |
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1076 |
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1077 - name: tmpdirMin |
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1078 type: ["null", long, Expression] |
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1079 doc: Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024) |
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1080 |
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1081 - name: tmpdirMax |
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1082 type: ["null", long, Expression] |
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1083 doc: Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) |
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1084 |
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1085 - name: outdirMin |
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1086 type: ["null", long, Expression] |
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1087 doc: Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024) |
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1088 |
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1089 - name: outdirMax |
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1090 type: ["null", long, Expression] |
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1091 doc: Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) |
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1092 |
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1093 |
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1094 - type: record |
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1095 name: WorkReuse |
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1096 extends: ProcessRequirement |
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1097 doc: | |
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1098 For implementations that support reusing output from past work (on |
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1099 the assumption that same code and same input produce same |
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1100 results), control whether to enable or disable the reuse behavior |
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1101 for a particular tool or step (to accomodate situations where that |
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1102 assumption is incorrect). A reused step is not executed but |
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1103 instead returns the same output as the original execution. |
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1104 |
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1105 If `enableReuse` is not specified, correct tools should assume it |
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1106 is enabled by default. |
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1107 fields: |
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1108 - name: class |
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1109 type: string |
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1110 doc: "Always 'WorkReuse'" |
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1111 jsonldPredicate: |
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1112 "_id": "@type" |
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1113 "_type": "@vocab" |
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1114 - name: enableReuse |
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1115 type: [boolean, Expression] |
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1116 default: true |
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1117 |
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1118 |
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1119 - type: record |
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1120 name: NetworkAccess |
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1121 extends: ProcessRequirement |
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1122 doc: | |
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1123 Indicate whether a process requires outgoing IPv4/IPv6 network |
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1124 access. Choice of IPv4 or IPv6 is implementation and site |
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1125 specific, correct tools must support both. |
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1126 |
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1127 If `networkAccess` is false or not specified, tools must not |
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1128 assume network access, except for localhost (the loopback device). |
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1129 |
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1130 If `networkAccess` is true, the tool must be able to make outgoing |
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1131 connections to network resources. Resources may be on a private |
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1132 subnet or the public Internet. However, implementations and sites |
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1133 may apply their own security policies to restrict what is |
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1134 accessible by the tool. |
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1135 |
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1136 Enabling network access does not imply a publically routable IP |
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1137 address or the ability to accept inbound connections. |
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1138 |
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1139 fields: |
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1140 - name: class |
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1141 type: string |
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1142 doc: "Always 'NetworkAccess'" |
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1143 jsonldPredicate: |
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1144 "_id": "@type" |
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1145 "_type": "@vocab" |
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1146 - name: networkAccess |
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1147 type: [boolean, Expression] |
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1148 |
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1149 - name: InplaceUpdateRequirement |
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1150 type: record |
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1151 extends: cwl:ProcessRequirement |
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1152 doc: | |
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1153 |
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1154 If `inplaceUpdate` is true, then an implementation supporting this |
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1155 feature may permit tools to directly update files with `writable: |
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1156 true` in InitialWorkDirRequirement. That is, as an optimization, |
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1157 files may be destructively modified in place as opposed to copied |
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1158 and updated. |
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1159 |
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1160 An implementation must ensure that only one workflow step may |
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1161 access a writable file at a time. It is an error if a file which |
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1162 is writable by one workflow step file is accessed (for reading or |
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1163 writing) by any other workflow step running independently. |
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1164 However, a file which has been updated in a previous completed |
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1165 step may be used as input to multiple steps, provided it is |
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1166 read-only in every step. |
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1167 |
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1168 Workflow steps which modify a file must produce the modified file |
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1169 as output. Downstream steps which futher process the file must |
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1170 use the output of previous steps, and not refer to a common input |
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1171 (this is necessary for both ordering and correctness). |
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1172 |
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1173 Workflow authors should provide this in the `hints` section. The |
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1174 intent of this feature is that workflows produce the same results |
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1175 whether or not InplaceUpdateRequirement is supported by the |
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1176 implementation, and this feature is primarily available as an |
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1177 optimization for particular environments. |
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1178 |
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1179 Users and implementers should be aware that workflows that |
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1180 destructively modify inputs may not be repeatable or reproducible. |
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1181 In particular, enabling this feature implies that WorkReuse should |
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1182 not be enabled. |
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1183 |
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1184 fields: |
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1185 class: |
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1186 type: string |
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1187 doc: "Always 'InplaceUpdateRequirement'" |
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1188 jsonldPredicate: |
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1189 "_id": "@type" |
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1190 "_type": "@vocab" |
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1191 inplaceUpdate: |
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1192 type: boolean |
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1193 |
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1194 - type: record |
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1195 name: ToolTimeLimit |
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1196 extends: ProcessRequirement |
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1197 doc: | |
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1198 Set an upper limit on the execution time of a CommandLineTool. |
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1199 A CommandLineTool whose execution duration exceeds the time |
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1200 limit may be preemptively terminated and considered failed. |
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1201 May also be used by batch systems to make scheduling decisions. |
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1202 The execution duration excludes external operations, such as |
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1203 staging of files, pulling a docker image etc, and only counts |
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1204 wall-time for the execution of the command line itself. |
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1205 fields: |
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1206 - name: class |
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1207 type: string |
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1208 doc: "Always 'ToolTimeLimit'" |
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1209 jsonldPredicate: |
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1210 "_id": "@type" |
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1211 "_type": "@vocab" |
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1212 - name: timelimit |
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1213 type: [long, Expression] |
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1214 doc: | |
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1215 The time limit, in seconds. A time limit of zero means no |
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1216 time limit. Negative time limits are an error. |