Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.2.0-dev5/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 $graph: |
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8 |
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9 - name: CommandLineToolDoc |
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10 type: documentation |
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11 doc: |
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12 - | |
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13 # Common Workflow Language (CWL) Command Line Tool Description, v1.2.0-dev5 |
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14 |
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15 This version: |
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16 * https://w3id.org/cwl/v1.2.0-dev5/ |
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17 |
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18 Current version: |
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19 * https://w3id.org/cwl/ |
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20 - "\n\n" |
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21 - {$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-dev5 |
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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-dev5 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-dev5` to make use of new |
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46 syntax and features introduced in v1.2.0-dev5. 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-dev5. |
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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 * `ramMin`, `ramMax`, `tmpdirMin`, `tmpdirMax`, `outdirMin`, and `outdirMax` of |
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57 [ResourceRequirement](#ResourceRequirement) now accept floating point values. |
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58 * (CommandLineTool)[#CommandLineTool] can now express `intent` |
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59 with an identifier for the type of computational operation. |
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60 * Added conformance tests for order of operations evaluating `secondaryFiles` on input |
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61 and ensure that input and output secondaryFiles expressions can return a File object. |
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62 * Clarify there are no limits on the size of file literal `contents`. |
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63 * When using `loadContents` it now must fail when attempting to |
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64 load a file greater than 64 KiB instead of silently truncating |
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65 the data. |
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66 * Objects, arrays and numbers returned by parameter references |
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67 or expressions in `Dirent.entry` that are not a `File` or |
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68 `Directory` object (or array of such) are now specified to be |
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69 JSON serialized to produce file contents. |
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70 * Note that only enum and record types can be typedef-ed |
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71 * Added conformance tests for order of operations evaluating `secondaryFiles` on input |
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72 and ensure that input and output secondaryFiles expressions can return a File object. |
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73 * Escaping in [string interpolation](#String_Interpolation) has |
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74 been added to the specification along with conformance tests. |
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75 * It is now possible to have an absolute path in the `entryname` |
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76 field in |
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77 [InitialWorkDirRequirement](#InitialWorkDirRequirement) when |
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78 running in a mandatory container. Together with |
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79 `DockerRequirement.dockerOutputDirectory` this it possible to |
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80 control the locations of both input and output files when |
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81 running in containers. |
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82 * Specify default success/fail interpretation of exit codes when not given. |
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83 |
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84 See also the [CWL Workflow Description, v1.2.0-dev5 changelog](Workflow.html#Changelog). |
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85 For other changes since CWL v1.0, see the |
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86 [CWL Command Line Tool Description, v1.1 changelog](https://www.commonwl.org/v1.1/CommandLineTool.html#Changelog) |
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87 |
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88 ## Purpose |
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89 |
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90 Standalone programs are a flexible and interoperable form of code reuse. |
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91 Unlike monolithic applications, applications and analysis workflows which |
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92 are composed of multiple separate programs can be written in multiple |
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93 languages and execute concurrently on multiple hosts. However, POSIX |
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94 does not dictate computer-readable grammar or semantics for program input |
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95 and output, resulting in extremely diverse command line grammar and |
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96 input/output semantics among programs. This is a particular problem in |
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97 distributed computing (multi-node compute clusters) and virtualized |
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98 environments (such as Docker containers) where it is often necessary to |
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99 provision resources such as input files before executing the program. |
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100 |
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101 Often this gap is filled by hard coding program invocation and |
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102 implicitly assuming requirements will be met, or abstracting program |
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103 invocation with wrapper scripts or descriptor documents. Unfortunately, |
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104 where these approaches are application or platform specific it creates a |
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105 significant barrier to reproducibility and portability, as methods |
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106 developed for one platform must be manually ported to be used on new |
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107 platforms. Similarly it creates redundant work, as wrappers for popular |
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108 tools must be rewritten for each application or platform in use. |
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109 |
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110 The Common Workflow Language Command Line Tool Description is designed to |
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111 provide a common standard description of grammar and semantics for |
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112 invoking programs used in data-intensive fields such as Bioinformatics, |
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113 Chemistry, Physics, Astronomy, and Statistics. This specification |
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114 attempts to define a precise data and execution model for Command Line Tools that |
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115 can be implemented on a variety of computing platforms, ranging from a |
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116 single workstation to cluster, grid, cloud, and high performance |
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117 computing platforms. Details related to execution of these programs not |
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118 laid out in this specification are open to interpretation by the computing |
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119 platform implementing this specification. |
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120 |
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121 - {$include: concepts.md} |
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122 - {$include: invocation.md} |
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123 |
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124 |
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125 - type: record |
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126 name: EnvironmentDef |
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127 doc: | |
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128 Define an environment variable that will be set in the runtime environment |
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129 by the workflow platform when executing the command line tool. May be the |
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130 result of executing an expression, such as getting a parameter from input. |
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131 fields: |
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132 - name: envName |
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133 type: string |
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134 doc: The environment variable name |
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135 - name: envValue |
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136 type: [string, Expression] |
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137 doc: The environment variable value |
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138 |
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139 - type: record |
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140 name: CommandLineBinding |
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141 extends: InputBinding |
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142 docParent: "#CommandInputParameter" |
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143 doc: | |
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144 |
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145 When listed under `inputBinding` in the input schema, the term |
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146 "value" refers to the the corresponding value in the input object. For |
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147 binding objects listed in `CommandLineTool.arguments`, the term "value" |
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148 refers to the effective value after evaluating `valueFrom`. |
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149 |
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150 The binding behavior when building the command line depends on the data |
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151 type of the value. If there is a mismatch between the type described by |
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152 the input schema and the effective value, such as resulting from an |
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153 expression evaluation, an implementation must use the data type of the |
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154 effective value. |
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155 |
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156 - **string**: Add `prefix` and the string to the command line. |
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157 |
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158 - **number**: Add `prefix` and decimal representation to command line. |
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159 |
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160 - **boolean**: If true, add `prefix` to the command line. If false, add |
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161 nothing. |
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162 |
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163 - **File**: Add `prefix` and the value of |
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164 [`File.path`](#File) to the command line. |
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165 |
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166 - **Directory**: Add `prefix` and the value of |
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167 [`Directory.path`](#Directory) to the command line. |
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168 |
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169 - **array**: If `itemSeparator` is specified, add `prefix` and the join |
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170 the array into a single string with `itemSeparator` separating the |
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171 items. Otherwise first add `prefix`, then recursively process |
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172 individual elements. |
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173 If the array is empty, it does not add anything to command line. |
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174 |
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175 - **object**: Add `prefix` only, and recursively add object fields for |
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176 which `inputBinding` is specified. |
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177 |
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178 - **null**: Add nothing. |
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179 |
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180 fields: |
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181 - name: position |
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182 type: [ "null", int, Expression ] |
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183 doc: | |
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184 The sorting key. Default position is 0. If the inputBinding is |
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185 associated with an input parameter, then the value of `self` in the |
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186 expression will be the value of the input parameter. Input parameter |
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187 defaults (as specified by the `InputParameter.default` field) must be |
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188 applied before evaluating the expression. Expressions must return a |
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189 single value of type int or a null. |
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190 - name: prefix |
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191 type: string? |
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192 doc: "Command line prefix to add before the value." |
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193 - name: separate |
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194 type: boolean? |
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195 default: true |
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196 doc: | |
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197 If true (default), then the prefix and value must be added as separate |
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198 command line arguments; if false, prefix and value must be concatenated |
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199 into a single command line argument. |
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200 - name: itemSeparator |
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201 type: string? |
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202 doc: | |
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203 Join the array elements into a single string with the elements |
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204 separated by by `itemSeparator`. |
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205 - name: valueFrom |
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206 type: |
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207 - "null" |
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208 - string |
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209 - Expression |
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210 jsonldPredicate: "cwl:valueFrom" |
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211 doc: | |
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212 If `valueFrom` is a constant string value, use this as the value and |
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213 apply the binding rules above. |
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214 |
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215 If `valueFrom` is an expression, evaluate the expression to yield the |
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216 actual value to use to build the command line and apply the binding |
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217 rules above. If the inputBinding is associated with an input |
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218 parameter, the value of `self` in the expression will be the value of |
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219 the input parameter. Input parameter defaults (as specified by the |
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220 `InputParameter.default` field) must be applied before evaluating the |
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221 expression. |
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222 |
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223 If the value of the associated input parameter is `null`, `valueFrom` is |
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224 not evaluated and nothing is added to the command line. |
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225 |
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226 When a binding is part of the `CommandLineTool.arguments` field, |
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227 the `valueFrom` field is required. |
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228 |
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229 - name: shellQuote |
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230 type: boolean? |
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231 default: true |
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232 doc: | |
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233 If `ShellCommandRequirement` is in the requirements for the current command, |
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234 this controls whether the value is quoted on the command line (default is true). |
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235 Use `shellQuote: false` to inject metacharacters for operations such as pipes. |
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236 |
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237 If `shellQuote` is true or not provided, the implementation must not |
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238 permit interpretation of any shell metacharacters or directives. |
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239 |
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240 |
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241 - type: record |
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242 name: CommandOutputBinding |
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243 extends: LoadContents |
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244 doc: | |
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245 Describes how to generate an output parameter based on the files produced |
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246 by a CommandLineTool. |
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247 |
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248 The output parameter value is generated by applying these operations in the |
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249 following order: |
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250 |
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251 - glob |
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252 - loadContents |
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253 - outputEval |
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254 - secondaryFiles |
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255 fields: |
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256 - name: glob |
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257 type: |
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258 - "null" |
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259 - string |
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260 - Expression |
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261 - type: array |
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262 items: string |
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263 doc: | |
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264 Find files or directories relative to the output directory, using POSIX |
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265 glob(3) pathname matching. If an array is provided, find files or |
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266 directories that match any pattern in the array. If an expression is |
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267 provided, the expression must return a string or an array of strings, |
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268 which will then be evaluated as one or more glob patterns. Must only |
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269 match and return files/directories which actually exist. |
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270 |
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271 If the value of glob is a relative path pattern (does not |
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272 begin with a slash '/') then it is resolved relative to the |
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273 output directory. If the value of the glob is an absolute |
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274 path pattern (it does begin with a slash '/') then it must |
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275 refer to a path within the output directory. It is an error |
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276 if any glob resolves to a path outside the output directory. |
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277 Specifically this means globs that resolve to paths outside the output |
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278 directory are illegal. |
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279 |
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280 A glob may match a path within the output directory which is |
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281 actually a symlink to another file. In this case, the |
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282 expected behavior is for the resulting File/Directory object to take the |
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283 `basename` (and corresponding `nameroot` and `nameext`) of the |
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284 symlink. The `location` of the File/Directory is implementation |
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285 dependent, but logically the File/Directory should have the same content |
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286 as the symlink target. Platforms may stage output files/directories to |
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287 cloud storage that lack the concept of a symlink. In |
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288 this case file content and directories may be duplicated, or (to avoid |
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289 duplication) the File/Directory `location` may refer to the symlink |
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290 target. |
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291 |
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292 It is an error if a symlink in the output directory (or any |
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293 symlink in a chain of links) refers to any file or directory |
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294 that is not under an input or output directory. |
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295 |
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296 Implementations may shut down a container before globbing |
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297 output, so globs and expressions must not assume access to the |
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298 container filesystem except for declared input and output. |
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299 |
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300 - name: outputEval |
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301 type: Expression? |
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302 doc: | |
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303 Evaluate an expression to generate the output value. If |
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304 `glob` was specified, the value of `self` must be an array |
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305 containing file objects that were matched. If no files were |
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306 matched, `self` must be a zero length array; if a single file |
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307 was matched, the value of `self` is an array of a single |
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308 element. The exit code of the process is |
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309 available in the expression as `runtime.exitCode`. |
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310 |
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311 Additionally if `loadContents` is true, the file must be a |
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312 UTF-8 text file 64 KiB or smaller, and the implementation must |
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313 read the entire contents of the file (or file array) and place |
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314 it in the `contents` field of the File object for use in |
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315 `outputEval`. If the size of the file is greater than 64 KiB, |
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316 the implementation must raise a fatal error. |
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317 |
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318 If a tool needs to return a large amount of structured data to |
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319 the workflow, loading the output object from `cwl.output.json` |
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320 bypasses `outputEval` and is not subject to the 64 KiB |
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321 `loadContents` limit. |
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322 |
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323 - name: CommandLineBindable |
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324 type: record |
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325 fields: |
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326 inputBinding: |
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327 type: CommandLineBinding? |
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328 jsonldPredicate: "cwl:inputBinding" |
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329 doc: Describes how to turn this object into command line arguments. |
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330 |
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331 - name: CommandInputRecordField |
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332 type: record |
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333 extends: [InputRecordField, CommandLineBindable] |
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334 specialize: |
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335 - specializeFrom: InputRecordSchema |
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|
336 specializeTo: CommandInputRecordSchema |
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|
337 - specializeFrom: InputEnumSchema |
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|
338 specializeTo: CommandInputEnumSchema |
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|
339 - specializeFrom: InputArraySchema |
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|
340 specializeTo: CommandInputArraySchema |
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|
341 - specializeFrom: InputBinding |
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|
342 specializeTo: CommandLineBinding |
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changeset
|
343 |
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changeset
|
344 |
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|
345 - name: CommandInputRecordSchema |
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|
346 type: record |
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|
347 extends: [InputRecordSchema, CommandInputSchema, CommandLineBindable] |
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|
348 specialize: |
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|
349 - specializeFrom: InputRecordField |
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|
350 specializeTo: CommandInputRecordField |
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|
351 - specializeFrom: InputBinding |
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|
352 specializeTo: CommandLineBinding |
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changeset
|
353 |
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changeset
|
354 |
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|
355 - name: CommandInputEnumSchema |
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|
356 type: record |
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|
357 extends: [InputEnumSchema, CommandInputSchema, CommandLineBindable] |
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|
358 specialize: |
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|
359 - specializeFrom: InputBinding |
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|
360 specializeTo: CommandLineBinding |
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changeset
|
361 |
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changeset
|
362 |
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|
363 - name: CommandInputArraySchema |
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|
364 type: record |
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|
365 extends: [InputArraySchema, CommandInputSchema, CommandLineBindable] |
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|
366 specialize: |
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|
367 - specializeFrom: InputRecordSchema |
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|
368 specializeTo: CommandInputRecordSchema |
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|
369 - specializeFrom: InputEnumSchema |
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|
370 specializeTo: CommandInputEnumSchema |
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|
371 - specializeFrom: InputArraySchema |
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|
372 specializeTo: CommandInputArraySchema |
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|
373 - specializeFrom: InputBinding |
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|
374 specializeTo: CommandLineBinding |
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|
375 |
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|
376 |
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|
377 - name: CommandOutputRecordField |
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|
378 type: record |
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|
379 extends: OutputRecordField |
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|
380 specialize: |
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|
381 - specializeFrom: OutputRecordSchema |
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|
382 specializeTo: CommandOutputRecordSchema |
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|
383 - specializeFrom: OutputEnumSchema |
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|
384 specializeTo: CommandOutputEnumSchema |
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|
385 - specializeFrom: OutputArraySchema |
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|
386 specializeTo: CommandOutputArraySchema |
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|
387 fields: |
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|
388 - name: outputBinding |
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|
389 type: CommandOutputBinding? |
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|
390 jsonldPredicate: "cwl:outputBinding" |
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|
391 doc: | |
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|
392 Describes how to generate this output object based on the files |
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|
393 produced by a CommandLineTool |
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|
394 |
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|
395 |
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|
396 - name: CommandOutputRecordSchema |
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|
397 type: record |
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|
398 extends: OutputRecordSchema |
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|
399 specialize: |
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|
400 - specializeFrom: OutputRecordField |
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|
401 specializeTo: CommandOutputRecordField |
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|
402 |
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|
403 |
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|
404 - name: CommandOutputEnumSchema |
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|
405 type: record |
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|
406 extends: OutputEnumSchema |
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|
407 specialize: |
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|
408 - specializeFrom: OutputRecordSchema |
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|
409 specializeTo: CommandOutputRecordSchema |
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|
410 - specializeFrom: OutputEnumSchema |
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|
411 specializeTo: CommandOutputEnumSchema |
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|
412 - specializeFrom: OutputArraySchema |
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|
413 specializeTo: CommandOutputArraySchema |
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|
414 |
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|
415 |
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|
416 - name: CommandOutputArraySchema |
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|
417 type: record |
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|
418 extends: OutputArraySchema |
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|
419 specialize: |
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|
420 - specializeFrom: OutputRecordSchema |
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|
421 specializeTo: CommandOutputRecordSchema |
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|
422 - specializeFrom: OutputEnumSchema |
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|
423 specializeTo: CommandOutputEnumSchema |
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|
424 - specializeFrom: OutputArraySchema |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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|
425 specializeTo: CommandOutputArraySchema |
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parents:
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|
426 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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|
427 |
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|
428 - type: record |
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|
429 name: CommandInputParameter |
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|
430 extends: InputParameter |
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|
431 doc: An input parameter for a CommandLineTool. |
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|
432 fields: |
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|
433 - name: type |
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|
434 type: |
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|
435 - CWLType |
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|
436 - stdin |
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|
437 - CommandInputRecordSchema |
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|
438 - CommandInputEnumSchema |
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|
439 - CommandInputArraySchema |
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|
440 - string |
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|
441 - type: array |
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|
442 items: |
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|
443 - CWLType |
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|
444 - CommandInputRecordSchema |
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|
445 - CommandInputEnumSchema |
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|
446 - CommandInputArraySchema |
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changeset
|
447 - string |
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|
448 jsonldPredicate: |
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|
449 "_id": "sld:type" |
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|
450 "_type": "@vocab" |
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|
451 refScope: 2 |
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|
452 typeDSL: True |
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453 doc: | |
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454 Specify valid types of data that may be assigned to this parameter. |
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455 - name: inputBinding |
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456 type: CommandLineBinding? |
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457 doc: | |
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458 Describes how to turns the input parameters of a process into |
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459 command line arguments. |
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460 jsonldPredicate: "cwl:inputBinding" |
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461 |
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462 - type: record |
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463 name: CommandOutputParameter |
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464 extends: OutputParameter |
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465 doc: An output parameter for a CommandLineTool. |
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466 fields: |
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467 - name: type |
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468 type: |
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469 - CWLType |
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470 - stdout |
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471 - stderr |
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472 - CommandOutputRecordSchema |
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473 - CommandOutputEnumSchema |
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474 - CommandOutputArraySchema |
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475 - string |
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476 - type: array |
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477 items: |
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478 - CWLType |
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479 - CommandOutputRecordSchema |
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480 - CommandOutputEnumSchema |
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481 - CommandOutputArraySchema |
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482 - string |
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483 jsonldPredicate: |
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484 "_id": "sld:type" |
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485 "_type": "@vocab" |
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486 refScope: 2 |
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487 typeDSL: True |
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488 doc: | |
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489 Specify valid types of data that may be assigned to this parameter. |
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490 - name: outputBinding |
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491 type: CommandOutputBinding? |
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492 jsonldPredicate: "cwl:outputBinding" |
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493 doc: Describes how to generate this output object based on the files |
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494 produced by a CommandLineTool |
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495 |
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496 - name: stdin |
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497 type: enum |
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498 symbols: [ "cwl:stdin" ] |
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499 docParent: "#CommandOutputParameter" |
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500 doc: | |
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501 Only valid as a `type` for a `CommandLineTool` input with no |
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502 `inputBinding` set. `stdin` must not be specified at the `CommandLineTool` |
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503 level. |
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504 |
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505 The following |
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506 ``` |
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507 inputs: |
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508 an_input_name: |
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509 type: stdin |
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510 ``` |
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511 is equivalent to |
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512 ``` |
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513 inputs: |
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514 an_input_name: |
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515 type: File |
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516 streamable: true |
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517 |
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518 stdin: ${inputs.an_input_name.path} |
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519 ``` |
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520 |
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521 - name: stdout |
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522 type: enum |
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523 symbols: [ "cwl:stdout" ] |
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524 docParent: "#CommandOutputParameter" |
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525 doc: | |
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526 Only valid as a `type` for a `CommandLineTool` output with no |
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527 `outputBinding` set. |
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528 |
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529 The following |
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530 ``` |
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531 outputs: |
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532 an_output_name: |
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533 type: stdout |
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534 |
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535 stdout: a_stdout_file |
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536 ``` |
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537 is equivalent to |
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538 ``` |
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539 outputs: |
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540 an_output_name: |
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541 type: File |
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542 streamable: true |
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543 outputBinding: |
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544 glob: a_stdout_file |
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545 |
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546 stdout: a_stdout_file |
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547 ``` |
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548 |
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549 If there is no `stdout` name provided, a random filename will be created. |
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550 For example, the following |
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551 ``` |
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552 outputs: |
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553 an_output_name: |
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554 type: stdout |
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555 ``` |
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556 is equivalent to |
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557 ``` |
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558 outputs: |
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559 an_output_name: |
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560 type: File |
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561 streamable: true |
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562 outputBinding: |
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563 glob: random_stdout_filenameABCDEFG |
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564 |
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565 stdout: random_stdout_filenameABCDEFG |
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566 ``` |
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567 |
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568 |
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569 - name: stderr |
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570 type: enum |
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571 symbols: [ "cwl:stderr" ] |
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572 docParent: "#CommandOutputParameter" |
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573 doc: | |
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574 Only valid as a `type` for a `CommandLineTool` output with no |
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575 `outputBinding` set. |
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576 |
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577 The following |
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578 ``` |
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579 outputs: |
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580 an_output_name: |
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581 type: stderr |
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582 |
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583 stderr: a_stderr_file |
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584 ``` |
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585 is equivalent to |
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586 ``` |
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587 outputs: |
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588 an_output_name: |
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589 type: File |
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590 streamable: true |
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591 outputBinding: |
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592 glob: a_stderr_file |
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593 |
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594 stderr: a_stderr_file |
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595 ``` |
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596 |
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597 If there is no `stderr` name provided, a random filename will be created. |
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598 For example, the following |
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599 ``` |
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600 outputs: |
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601 an_output_name: |
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602 type: stderr |
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603 ``` |
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604 is equivalent to |
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605 ``` |
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606 outputs: |
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607 an_output_name: |
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608 type: File |
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609 streamable: true |
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610 outputBinding: |
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611 glob: random_stderr_filenameABCDEFG |
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612 |
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613 stderr: random_stderr_filenameABCDEFG |
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614 ``` |
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615 |
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616 |
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617 - type: record |
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618 name: CommandLineTool |
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619 extends: Process |
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620 documentRoot: true |
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621 specialize: |
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622 - specializeFrom: InputParameter |
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623 specializeTo: CommandInputParameter |
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624 - specializeFrom: OutputParameter |
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625 specializeTo: CommandOutputParameter |
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626 doc: | |
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627 This defines the schema of the CWL Command Line Tool Description document. |
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628 |
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629 fields: |
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630 - name: class |
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631 jsonldPredicate: |
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632 "_id": "@type" |
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633 "_type": "@vocab" |
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634 type: string |
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635 - name: baseCommand |
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636 doc: | |
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637 Specifies the program to execute. If an array, the first element of |
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638 the array is the command to execute, and subsequent elements are |
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639 mandatory command line arguments. The elements in `baseCommand` must |
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640 appear before any command line bindings from `inputBinding` or |
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641 `arguments`. |
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642 |
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643 If `baseCommand` is not provided or is an empty array, the first |
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644 element of the command line produced after processing `inputBinding` or |
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645 `arguments` must be used as the program to execute. |
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646 |
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647 If the program includes a path separator character it must |
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648 be an absolute path, otherwise it is an error. If the program does not |
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649 include a path separator, search the `$PATH` variable in the runtime |
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650 environment of the workflow runner find the absolute path of the |
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651 executable. |
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652 type: |
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653 - string? |
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654 - string[]? |
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655 jsonldPredicate: |
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656 "_id": "cwl:baseCommand" |
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657 "_container": "@list" |
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658 - name: arguments |
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659 doc: | |
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660 Command line bindings which are not directly associated with input |
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661 parameters. If the value is a string, it is used as a string literal |
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662 argument. If it is an Expression, the result of the evaluation is used |
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663 as an argument. |
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664 type: |
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665 - "null" |
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666 - type: array |
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667 items: [string, Expression, CommandLineBinding] |
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668 jsonldPredicate: |
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669 "_id": "cwl:arguments" |
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670 "_container": "@list" |
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671 - name: stdin |
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672 type: ["null", string, Expression] |
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673 jsonldPredicate: "https://w3id.org/cwl/cwl#stdin" |
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674 doc: | |
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675 A path to a file whose contents must be piped into the command's |
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676 standard input stream. |
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677 - name: stderr |
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678 type: ["null", string, Expression] |
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679 jsonldPredicate: "https://w3id.org/cwl/cwl#stderr" |
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680 doc: | |
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681 Capture the command's standard error stream to a file written to |
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682 the designated output directory. |
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683 |
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684 If `stderr` is a string, it specifies the file name to use. |
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685 |
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686 If `stderr` is an expression, the expression is evaluated and must |
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687 return a string with the file name to use to capture stderr. If the |
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688 return value is not a string, or the resulting path contains illegal |
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689 characters (such as the path separator `/`) it is an error. |
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690 - name: stdout |
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691 type: ["null", string, Expression] |
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692 jsonldPredicate: "https://w3id.org/cwl/cwl#stdout" |
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693 doc: | |
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694 Capture the command's standard output stream to a file written to |
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695 the designated output directory. |
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696 |
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697 If `stdout` is a string, it specifies the file name to use. |
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698 |
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699 If `stdout` is an expression, the expression is evaluated and must |
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700 return a string with the file name to use to capture stdout. If the |
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701 return value is not a string, or the resulting path contains illegal |
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702 characters (such as the path separator `/`) it is an error. |
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703 - name: successCodes |
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704 type: int[]? |
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705 doc: | |
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706 Exit codes that indicate the process completed successfully. |
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707 |
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708 If not specified, only exit code 0 is considered success. |
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709 |
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710 - name: temporaryFailCodes |
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711 type: int[]? |
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712 doc: | |
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713 Exit codes that indicate the process failed due to a possibly |
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714 temporary condition, where executing the process with the same |
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715 runtime environment and inputs may produce different results. |
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716 |
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717 If not specified, no exit codes are considered temporary failure. |
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718 |
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719 - name: permanentFailCodes |
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720 type: int[]? |
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721 doc: |
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722 Exit codes that indicate the process failed due to a permanent logic |
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723 error, where executing the process with the same runtime environment and |
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724 same inputs is expected to always fail. |
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725 |
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726 If not specified, all exit codes except 0 are considered permanent failure. |
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727 |
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728 |
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729 - type: record |
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730 name: DockerRequirement |
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731 extends: ProcessRequirement |
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732 doc: | |
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733 Indicates that a workflow component should be run in a |
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734 [Docker](http://docker.com) or Docker-compatible (such as |
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735 [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and |
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736 specifies how to fetch or build the image. |
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737 |
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738 If a CommandLineTool lists `DockerRequirement` under |
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739 `hints` (or `requirements`), it may (or must) be run in the specified Docker |
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740 container. |
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741 |
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742 The platform must first acquire or install the correct Docker image as |
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743 specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`. |
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744 |
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745 The platform must execute the tool in the container using `docker run` with |
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746 the appropriate Docker image and tool command line. |
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747 |
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748 The workflow platform may provide input files and the designated output |
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749 directory through the use of volume bind mounts. The platform should rewrite |
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750 file paths in the input object to correspond to the Docker bind mounted |
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751 locations. That is, the platform should rewrite values in the parameter context |
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752 such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths |
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753 within the container. The platform must ensure that `runtime.outdir` and |
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754 `runtime.tmpdir` are distinct directories. |
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755 |
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756 When running a tool contained in Docker, the workflow platform must not |
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757 assume anything about the contents of the Docker container, such as the |
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758 presence or absence of specific software, except to assume that the |
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759 generated command line represents a valid command within the runtime |
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760 environment of the container. |
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761 |
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762 A container image may specify an |
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763 [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint) |
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764 and/or |
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765 [CMD](https://docs.docker.com/engine/reference/builder/#cmd). |
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766 Command line arguments will be appended after all elements of |
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767 ENTRYPOINT, and will override all elements specified using CMD (in |
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768 other words, CMD is only used when the CommandLineTool definition |
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769 produces an empty command line). |
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770 |
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771 Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility |
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772 concerns of the implicit hidden execution point (For further discussion, see |
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773 [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable |
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774 CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. |
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775 CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the |
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776 `requirements` section. |
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777 |
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778 ## Interaction with other requirements |
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779 |
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780 If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a |
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781 DockerRequirement, the environment variables must be provided to Docker |
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782 using `--env` or `--env-file` and interact with the container's preexisting |
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783 environment as defined by Docker. |
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784 |
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785 fields: |
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786 - name: class |
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787 type: string |
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788 doc: "Always 'DockerRequirement'" |
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789 jsonldPredicate: |
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790 "_id": "@type" |
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791 "_type": "@vocab" |
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792 - name: dockerPull |
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793 type: string? |
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794 doc: | |
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795 Specify a Docker image to retrieve using `docker pull`. Can contain the |
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796 immutable digest to ensure an exact container is used: |
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797 `dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2` |
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798 - name: dockerLoad |
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799 type: string? |
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800 doc: "Specify a HTTP URL from which to download a Docker image using `docker load`." |
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801 - name: dockerFile |
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802 type: string? |
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803 doc: "Supply the contents of a Dockerfile which will be built using `docker build`." |
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804 - name: dockerImport |
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805 type: string? |
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|
806 doc: "Provide HTTP URL to download and gunzip a Docker images using `docker import." |
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807 - name: dockerImageId |
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808 type: string? |
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809 doc: | |
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810 The image id that will be used for `docker run`. May be a |
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811 human-readable image name or the image identifier hash. May be skipped |
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|
812 if `dockerPull` is specified, in which case the `dockerPull` image id |
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813 must be used. |
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814 - name: dockerOutputDirectory |
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815 type: string? |
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816 doc: | |
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817 Set the designated output directory to a specific location inside the |
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818 Docker container. |
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819 |
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820 |
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821 - type: record |
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822 name: SoftwareRequirement |
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823 extends: ProcessRequirement |
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824 doc: | |
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825 A list of software packages that should be configured in the environment of |
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826 the defined process. |
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827 fields: |
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828 - name: class |
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829 type: string |
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830 doc: "Always 'SoftwareRequirement'" |
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831 jsonldPredicate: |
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832 "_id": "@type" |
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833 "_type": "@vocab" |
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834 - name: packages |
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835 type: SoftwarePackage[] |
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836 doc: "The list of software to be configured." |
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837 jsonldPredicate: |
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838 mapSubject: package |
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839 mapPredicate: specs |
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840 |
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841 - name: SoftwarePackage |
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842 type: record |
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|
843 fields: |
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844 - name: package |
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845 type: string |
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846 doc: | |
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847 The name of the software to be made available. If the name is |
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848 common, inconsistent, or otherwise ambiguous it should be combined with |
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849 one or more identifiers in the `specs` field. |
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850 - name: version |
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|
851 type: string[]? |
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852 doc: | |
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853 The (optional) versions of the software that are known to be |
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|
854 compatible. |
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855 - name: specs |
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856 type: string[]? |
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|
857 jsonldPredicate: {_type: "@id", noLinkCheck: true} |
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858 doc: | |
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859 One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s |
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860 identifying resources for installing or enabling the software named in |
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861 the `package` field. Implementations may provide resolvers which map |
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|
862 these software identifer IRIs to some configuration action; or they can |
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863 use only the name from the `package` field on a best effort basis. |
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|
864 |
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865 For example, the IRI https://packages.debian.org/bowtie could |
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866 be resolved with `apt-get install bowtie`. The IRI |
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867 https://anaconda.org/bioconda/bowtie could be resolved with `conda |
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868 install -c bioconda bowtie`. |
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|
869 |
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870 IRIs can also be system independent and used to map to a specific |
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871 software installation or selection mechanism. |
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872 Using [RRID](https://www.identifiers.org/rrid/) as an example: |
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873 https://identifiers.org/rrid/RRID:SCR_005476 |
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|
874 could be fulfilled using the above mentioned Debian or bioconda |
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875 package, a local installation managed by [Environement Modules](http://modules.sourceforge.net/), |
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876 or any other mechanism the platform chooses. IRIs can also be from |
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877 identifer sources that are discipline specific yet still system |
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878 independent. As an example, the equivalent [ELIXIR Tools and Data |
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879 Service Registry](https://bio.tools) IRI to the previous RRID example is |
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880 https://bio.tools/tool/bowtie2/version/2.2.8. |
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881 If supported by a given registry, implementations are encouraged to |
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882 query these system independent sofware identifier IRIs directly for |
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883 links to packaging systems. |
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|
884 |
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885 A site specific IRI can be listed as well. For example, an academic |
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886 computing cluster using Environement Modules could list the IRI |
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887 `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that |
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888 `module load bowtie-tbb/1.1.2` should be executed to make available |
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889 `bowtie` version 1.1.2 compiled with the TBB library prior to running |
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890 the accompanying Workflow or CommandLineTool. Note that the example IRI |
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891 is specific to a particular institution and computing environment as |
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892 the Environment Modules system does not have a common namespace or |
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893 standardized naming convention. |
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|
894 |
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895 This last example is the least portable and should only be used if |
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896 mechanisms based off of the `package` field or more generic IRIs are |
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897 unavailable or unsuitable. While harmless to other sites, site specific |
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898 software IRIs should be left out of shared CWL descriptions to avoid |
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899 clutter. |
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|
900 |
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|
901 - name: Dirent |
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902 type: record |
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|
903 doc: | |
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904 Define a file or subdirectory that must be staged to a particular |
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905 place prior to executing the command line tool. May be the result |
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906 of executing an expression, such as building a configuration file |
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907 from a template. |
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|
908 |
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909 Usually files are staged within the [designated output directory](#Runtime_environment). |
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910 However, under certain circumstances, files may be staged at |
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|
911 arbitrary locations, see discussion for `entryname`. |
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|
912 |
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|
913 fields: |
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|
914 - name: entryname |
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|
915 type: ["null", string, Expression] |
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|
916 jsonldPredicate: |
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|
917 _id: cwl:entryname |
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|
918 doc: | |
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|
919 The "target" name of the file or subdirectory. If `entry` is |
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|
920 a File or Directory, the `entryname` field overrides the value |
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|
921 of `basename` of the File or Directory object. |
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|
922 |
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|
923 * Required when `entry` evaluates to file contents only |
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|
924 * Optional when `entry` evaluates to a File or Directory object with a `basename` |
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|
925 * Invalid when `entry` evaluates to an array of File or Directory objects. |
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|
926 |
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|
927 If `entryname` is a relative path, it specifies a name within |
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|
928 the designated output directory. A relative path starting |
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929 with `../` or that resolves to location above the designated output directory is an error. |
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|
930 |
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|
931 If `entryname` is an absolute path (starts with a slash `/`) |
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|
932 it is an error unless the following conditions are met: |
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|
933 |
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|
934 * `DockerRequirement` is present in `requirements` |
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|
935 * The program is will run inside a software container |
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|
936 where, from the perspective of the program, the root |
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|
937 filesystem is not shared with any other user or |
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|
938 running program. |
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|
939 |
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|
940 In this case, and the above conditions are met, then |
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|
941 `entryname` may specify the absolute path within the container |
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|
942 where the file or directory must be placed. |
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943 |
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944 - name: entry |
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|
945 type: [string, Expression] |
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946 jsonldPredicate: |
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|
947 _id: cwl:entry |
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948 doc: | |
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949 If the value is a string literal or an expression which evaluates to a |
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|
950 string, a new text file must be created with the string as the file contents. |
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|
951 |
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952 If the value is an expression that evaluates to a `File` or |
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|
953 `Directory` object, or an array of `File` or `Directory` |
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|
954 objects, this indicates the referenced file or directory |
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|
955 should be added to the designated output directory prior to |
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|
956 executing the tool. |
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|
957 |
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958 If the value is an expression that evaluates to `null`, |
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|
959 nothing is added to the designated output directory, the entry |
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|
960 has no effect. |
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961 |
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962 If the value is an expression that evaluates to some other |
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963 array, number, or object not consisting of `File` or |
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964 `Directory` objects, a new file must be created with the value |
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965 serialized to JSON text as the file contents. The JSON |
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966 serialization behavior should match the behavior of string |
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967 interpolation of [Parameter |
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968 references](#Parameter_references). |
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969 |
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970 - name: writable |
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971 type: boolean? |
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972 default: false |
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973 doc: | |
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974 If true, the File or Directory (or array of Files or |
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975 Directories) declared in `entry` must be writable by the tool. |
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976 |
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977 Changes to the file or directory must be isolated and not |
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|
978 visible by any other CommandLineTool process. This may be |
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979 implemented by making a copy of the original file or |
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980 directory. |
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981 |
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982 Default false (files and directories read-only by default). |
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983 |
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984 A directory marked as `writable: true` implies that all files and |
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985 subdirectories are recursively writable as well. |
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986 |
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987 If `writable` is false, the file may be made available using a |
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988 bind mount or file system link to avoid unnecessary copying of |
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989 the input file. Command line tools may receive an error on |
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990 attempting to rename or delete files or directories that are |
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991 not explicitly marked as writable. |
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992 |
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993 |
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994 - name: InitialWorkDirRequirement |
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995 type: record |
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996 extends: ProcessRequirement |
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997 doc: |
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998 Define a list of files and subdirectories that must be staged by |
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999 the workflow platform prior to executing the command line tool. |
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1000 |
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1001 Normally files are staged within the designated output directory. |
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1002 However, when running inside containers, files may be staged at |
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1003 arbitrary locations, see discussion for `Dirent.entryname`. |
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1004 Together with `DockerRequirement.dockerOutputDirectory` this it |
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1005 possible to control the locations of both input and output files |
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1006 when running in containers. |
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1007 |
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1008 fields: |
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1009 - name: class |
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1010 type: string |
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1011 doc: InitialWorkDirRequirement |
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1012 jsonldPredicate: |
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1013 "_id": "@type" |
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1014 "_type": "@vocab" |
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1015 - name: listing |
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1016 type: |
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1017 - Expression |
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1018 - type: array |
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1019 items: |
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1020 - "null" |
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1021 - Dirent |
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1022 - Expression |
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1023 - File |
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1024 - Directory |
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1025 - type: array |
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1026 items: |
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1027 - File |
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1028 - Directory |
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1029 jsonldPredicate: |
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1030 _id: "cwl:listing" |
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1031 doc: | |
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1032 The list of files or subdirectories that must be staged prior |
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1033 to executing the command line tool. |
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1034 |
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1035 Return type of each expression must validate as `["null", |
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1036 File, Directory, Dirent, {type: array, items: [File, |
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1037 Directory]}]`. |
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|
1038 |
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1039 Each `File` or `Directory` that is returned by an Expression |
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1040 must be added to the designated output directory prior to |
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1041 executing the tool. |
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1042 |
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1043 Each `Dirent` record that is listed or returned by an |
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1044 expression specifies a file to be created or staged in the |
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1045 designated output directory prior to executing the tool. |
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1046 |
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1047 Expressions may return null, in which case they have no effect. |
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1048 |
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1049 Files or Directories which are listed in the input parameters |
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1050 and appear in the `InitialWorkDirRequirement` listing must |
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1051 have their `path` set to their staged location. If the same |
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1052 File or Directory appears more than once in the |
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1053 `InitialWorkDirRequirement` listing, the implementation must |
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1054 choose exactly one value for `path`; how this value is chosen |
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1055 is undefined. |
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1056 |
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1057 |
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1058 - name: EnvVarRequirement |
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1059 type: record |
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1060 extends: ProcessRequirement |
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1061 doc: | |
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1062 Define a list of environment variables which will be set in the |
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1063 execution environment of the tool. See `EnvironmentDef` for details. |
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1064 fields: |
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1065 - name: class |
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1066 type: string |
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1067 doc: "Always 'EnvVarRequirement'" |
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1068 jsonldPredicate: |
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1069 "_id": "@type" |
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1070 "_type": "@vocab" |
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1071 - name: envDef |
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1072 type: EnvironmentDef[] |
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1073 doc: The list of environment variables. |
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1074 jsonldPredicate: |
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1075 mapSubject: envName |
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1076 mapPredicate: envValue |
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1077 |
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1078 |
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1079 - type: record |
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1080 name: ShellCommandRequirement |
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1081 extends: ProcessRequirement |
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1082 doc: | |
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1083 Modify the behavior of CommandLineTool to generate a single string |
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1084 containing a shell command line. Each item in the argument list must be |
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1085 joined into a string separated by single spaces and quoted to prevent |
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1086 intepretation by the shell, unless `CommandLineBinding` for that argument |
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1087 contains `shellQuote: false`. If `shellQuote: false` is specified, the |
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1088 argument is joined into the command string without quoting, which allows |
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1089 the use of shell metacharacters such as `|` for pipes. |
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1090 fields: |
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1091 - name: class |
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1092 type: string |
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1093 doc: "Always 'ShellCommandRequirement'" |
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1094 jsonldPredicate: |
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1095 "_id": "@type" |
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1096 "_type": "@vocab" |
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1097 |
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1098 |
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1099 - type: record |
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1100 name: ResourceRequirement |
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1101 extends: ProcessRequirement |
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1102 doc: | |
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1103 Specify basic hardware resource requirements. |
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1104 |
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1105 "min" is the minimum amount of a resource that must be reserved to |
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1106 schedule a job. If "min" cannot be satisfied, the job should not |
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1107 be run. |
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1108 |
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1109 "max" is the maximum amount of a resource that the job shall be |
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1110 allocated. If a node has sufficient resources, multiple jobs may |
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1111 be scheduled on a single node provided each job's "max" resource |
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1112 requirements are met. If a job attempts to exceed its resource |
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1113 allocation, an implementation may deny additional resources, which |
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1114 may result in job failure. |
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1115 |
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1116 If both "min" and "max" are specified, an implementation may |
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1117 choose to allocate any amount between "min" and "max", with the |
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1118 actual allocation provided in the `runtime` object. |
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1119 |
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1120 If "min" is specified but "max" is not, then "max" == "min" |
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1121 If "max" is specified by "min" is not, then "min" == "max". |
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1122 |
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1123 It is an error if max < min. |
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1124 |
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1125 It is an error if the value of any of these fields is negative. |
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1126 |
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1127 If neither "min" nor "max" is specified for a resource, use the default values below. |
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1128 |
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1129 fields: |
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1130 - name: class |
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1131 type: string |
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1132 doc: "Always 'ResourceRequirement'" |
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1133 jsonldPredicate: |
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1134 "_id": "@type" |
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1135 "_type": "@vocab" |
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1136 - name: coresMin |
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|
1137 type: ["null", long, float, Expression] |
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|
1138 doc: | |
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|
1139 Minimum reserved number of CPU cores (default is 1). |
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1140 |
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|
1141 May be a fractional value to indicate to a scheduling |
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|
1142 algorithm that one core can be allocated to multiple |
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|
1143 jobs. For example, a value of 0.25 indicates that up to 4 |
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|
1144 jobs may run in parallel on 1 core. A value of 1.25 means |
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|
1145 that up to 3 jobs can run on a 4 core system (4/1.25 ≈ 3). |
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|
1146 |
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|
1147 Processes can only share a core allocation if the sum of each |
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|
1148 of their `ramMax`, `tmpdirMax`, and `outdirMax` requests also |
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|
1149 do not exceed the capacity of the node. |
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|
1150 |
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|
1151 Processes sharing a core must have the same level of isolation |
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|
1152 (typically a container or VM) that they would normally. |
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1153 |
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|
1154 The reported number of CPU cores reserved for the process, |
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|
1155 which is available to expressions on the CommandLineTool as |
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|
1156 `runtime.cores`, must be a non-zero integer, and may be |
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|
1157 calculated by rounding up the cores request to the next whole |
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|
1158 number. |
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|
1159 |
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1160 Scheduling systems may allocate fractional CPU resources by |
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1161 setting quotas or scheduling weights. Scheduling systems that |
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1162 do not support fractional CPUs may round up the request to the |
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1163 next whole number. |
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1164 |
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1165 - name: coresMax |
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1166 type: ["null", long, float, Expression] |
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1167 doc: | |
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1168 Maximum reserved number of CPU cores. |
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1169 |
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1170 See `coresMin` for discussion about fractional CPU requests. |
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1171 |
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1172 - name: ramMin |
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1173 type: ["null", long, float, Expression] |
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1174 doc: | |
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1175 Minimum reserved RAM in mebibytes (2**20) (default is 256) |
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1176 |
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1177 May be a fractional value. If so, the actual RAM request must |
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1178 be rounded up to the next whole number. The reported amount of |
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1179 RAM reserved for the process, which is available to |
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1180 expressions on the CommandLineTool as `runtime.ram`, must be a |
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1181 non-zero integer. |
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|
1182 |
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1183 - name: ramMax |
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1184 type: ["null", long, float, Expression] |
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1185 doc: | |
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1186 Maximum reserved RAM in mebibytes (2**20) |
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1187 |
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|
1188 See `ramMin` for discussion about fractional RAM requests. |
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1189 |
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1190 - name: tmpdirMin |
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1191 type: ["null", long, float, Expression] |
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|
1192 doc: | |
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1193 Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024) |
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1194 |
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1195 May be a fractional value. If so, the actual storage request |
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|
1196 must be rounded up to the next whole number. The reported |
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|
1197 amount of storage reserved for the process, which is available |
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|
1198 to expressions on the CommandLineTool as `runtime.tmpdirSize`, |
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|
1199 must be a non-zero integer. |
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|
1200 |
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|
1201 - name: tmpdirMax |
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|
1202 type: ["null", long, float, Expression] |
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|
1203 doc: | |
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|
1204 Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) |
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1205 |
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|
1206 See `tmpdirMin` for discussion about fractional storage requests. |
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1207 |
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|
1208 - name: outdirMin |
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|
1209 type: ["null", long, float, Expression] |
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|
1210 doc: | |
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1211 Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024) |
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|
1212 |
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|
1213 May be a fractional value. If so, the actual storage request |
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|
1214 must be rounded up to the next whole number. The reported |
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|
1215 amount of storage reserved for the process, which is available |
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|
1216 to expressions on the CommandLineTool as `runtime.outdirSize`, |
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|
1217 must be a non-zero integer. |
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|
1218 |
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|
1219 - name: outdirMax |
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1220 type: ["null", long, float, Expression] |
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|
1221 doc: | |
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1222 Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) |
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|
1223 |
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1224 See `outdirMin` for discussion about fractional storage requests. |
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1225 |
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|
1226 |
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|
1227 - type: record |
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|
1228 name: WorkReuse |
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|
1229 extends: ProcessRequirement |
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|
1230 doc: | |
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1231 For implementations that support reusing output from past work (on |
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1232 the assumption that same code and same input produce same |
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|
1233 results), control whether to enable or disable the reuse behavior |
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|
1234 for a particular tool or step (to accomodate situations where that |
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1235 assumption is incorrect). A reused step is not executed but |
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|
1236 instead returns the same output as the original execution. |
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1237 |
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1238 If `WorkReuse` is not specified, correct tools should assume it |
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1239 is enabled by default. |
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|
1240 fields: |
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1241 - name: class |
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|
1242 type: string |
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1243 doc: "Always 'WorkReuse'" |
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1244 jsonldPredicate: |
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|
1245 "_id": "@type" |
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|
1246 "_type": "@vocab" |
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1247 - name: enableReuse |
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1248 type: [boolean, Expression] |
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1249 default: true |
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1250 |
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1251 |
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1252 - type: record |
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1253 name: NetworkAccess |
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1254 extends: ProcessRequirement |
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1255 doc: | |
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1256 Indicate whether a process requires outgoing IPv4/IPv6 network |
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1257 access. Choice of IPv4 or IPv6 is implementation and site |
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1258 specific, correct tools must support both. |
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1259 |
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1260 If `networkAccess` is false or not specified, tools must not |
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1261 assume network access, except for localhost (the loopback device). |
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1262 |
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1263 If `networkAccess` is true, the tool must be able to make outgoing |
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1264 connections to network resources. Resources may be on a private |
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1265 subnet or the public Internet. However, implementations and sites |
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1266 may apply their own security policies to restrict what is |
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1267 accessible by the tool. |
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1268 |
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1269 Enabling network access does not imply a publically routable IP |
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1270 address or the ability to accept inbound connections. |
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1271 |
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1272 fields: |
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1273 - name: class |
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1274 type: string |
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1275 doc: "Always 'NetworkAccess'" |
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1276 jsonldPredicate: |
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1277 "_id": "@type" |
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1278 "_type": "@vocab" |
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1279 - name: networkAccess |
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1280 type: [boolean, Expression] |
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1281 |
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1282 - name: InplaceUpdateRequirement |
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1283 type: record |
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1284 extends: cwl:ProcessRequirement |
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1285 doc: | |
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1286 |
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1287 If `inplaceUpdate` is true, then an implementation supporting this |
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1288 feature may permit tools to directly update files with `writable: |
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1289 true` in InitialWorkDirRequirement. That is, as an optimization, |
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1290 files may be destructively modified in place as opposed to copied |
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1291 and updated. |
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1292 |
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1293 An implementation must ensure that only one workflow step may |
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1294 access a writable file at a time. It is an error if a file which |
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1295 is writable by one workflow step file is accessed (for reading or |
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1296 writing) by any other workflow step running independently. |
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1297 However, a file which has been updated in a previous completed |
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1298 step may be used as input to multiple steps, provided it is |
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1299 read-only in every step. |
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1300 |
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1301 Workflow steps which modify a file must produce the modified file |
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1302 as output. Downstream steps which futher process the file must |
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1303 use the output of previous steps, and not refer to a common input |
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1304 (this is necessary for both ordering and correctness). |
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1305 |
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1306 Workflow authors should provide this in the `hints` section. The |
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1307 intent of this feature is that workflows produce the same results |
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1308 whether or not InplaceUpdateRequirement is supported by the |
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1309 implementation, and this feature is primarily available as an |
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1310 optimization for particular environments. |
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1311 |
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1312 Users and implementers should be aware that workflows that |
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1313 destructively modify inputs may not be repeatable or reproducible. |
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1314 In particular, enabling this feature implies that WorkReuse should |
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1315 not be enabled. |
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1316 |
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1317 fields: |
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1318 class: |
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1319 type: string |
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1320 doc: "Always 'InplaceUpdateRequirement'" |
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1321 jsonldPredicate: |
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1322 "_id": "@type" |
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1323 "_type": "@vocab" |
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1324 inplaceUpdate: |
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1325 type: boolean |
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1326 |
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1327 - type: record |
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1328 name: ToolTimeLimit |
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1329 extends: ProcessRequirement |
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1330 doc: | |
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1331 Set an upper limit on the execution time of a CommandLineTool. |
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1332 A CommandLineTool whose execution duration exceeds the time |
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1333 limit may be preemptively terminated and considered failed. |
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1334 May also be used by batch systems to make scheduling decisions. |
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1335 The execution duration excludes external operations, such as |
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1336 staging of files, pulling a docker image etc, and only counts |
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1337 wall-time for the execution of the command line itself. |
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1338 fields: |
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1339 - name: class |
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1340 type: string |
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1341 doc: "Always 'ToolTimeLimit'" |
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1342 jsonldPredicate: |
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1343 "_id": "@type" |
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1344 "_type": "@vocab" |
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1345 - name: timelimit |
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1346 type: [long, Expression] |
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1347 doc: | |
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1348 The time limit, in seconds. A time limit of zero means no |
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1349 time limit. Negative time limits are an error. |