Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.1.0-dev1/Process.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 sld: "https://w3id.org/cwl/salad#" |
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7 rdfs: "http://www.w3.org/2000/01/rdf-schema#" |
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8 |
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9 $graph: |
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10 |
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11 - name: "Common Workflow Language, v1.1.0-dev1" |
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12 type: documentation |
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13 doc: {$include: concepts.md} |
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14 |
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15 - $import: "salad/schema_salad/metaschema/metaschema_base.yml" |
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16 |
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17 - name: BaseTypesDoc |
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18 type: documentation |
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19 doc: | |
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20 ## Base types |
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21 docChild: |
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22 - "#CWLType" |
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23 - "#Process" |
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24 |
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25 - type: enum |
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26 name: CWLVersion |
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27 doc: "Version symbols for published CWL document versions." |
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28 symbols: |
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29 - cwl:draft-2 |
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30 - cwl:draft-3.dev1 |
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31 - cwl:draft-3.dev2 |
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32 - cwl:draft-3.dev3 |
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33 - cwl:draft-3.dev4 |
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34 - cwl:draft-3.dev5 |
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35 - cwl:draft-3 |
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36 - cwl:draft-4.dev1 |
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37 - cwl:draft-4.dev2 |
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38 - cwl:draft-4.dev3 |
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39 - cwl:v1.0.dev4 |
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40 - cwl:v1.0 |
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41 - cwl:v1.1.0-dev1 # a dash is required by the semver 2.0 rules |
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42 |
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43 - name: CWLType |
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44 type: enum |
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45 extends: "sld:PrimitiveType" |
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46 symbols: |
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47 - cwl:File |
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48 - cwl:Directory |
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49 doc: |
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50 - "Extends primitive types with the concept of a file and directory as a builtin type." |
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51 - "File: A File object" |
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52 - "Directory: A Directory object" |
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53 |
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54 - name: File |
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55 type: record |
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56 docParent: "#CWLType" |
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57 doc: | |
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58 Represents a file (or group of files when `secondaryFiles` is provided) that |
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59 will be accessible by tools using standard POSIX file system call API such as |
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60 open(2) and read(2). |
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61 |
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62 Files are represented as objects with `class` of `File`. File objects have |
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63 a number of properties that provide metadata about the file. |
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64 |
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65 The `location` property of a File is a URI that uniquely identifies the |
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66 file. Implementations must support the file:// URI scheme and may support |
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67 other schemes such as http://. The value of `location` may also be a |
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68 relative reference, in which case it must be resolved relative to the URI |
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69 of the document it appears in. Alternately to `location`, implementations |
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70 must also accept the `path` property on File, which must be a filesystem |
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71 path available on the same host as the CWL runner (for inputs) or the |
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72 runtime environment of a command line tool execution (for command line tool |
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73 outputs). |
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74 |
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75 If no `location` or `path` is specified, a file object must specify |
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76 `contents` with the UTF-8 text content of the file. This is a "file |
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77 literal". File literals do not correspond to external resources, but are |
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78 created on disk with `contents` with when needed for a executing a tool. |
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79 Where appropriate, expressions can return file literals to define new files |
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80 on a runtime. The maximum size of `contents` is 64 kilobytes. |
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81 |
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82 The `basename` property defines the filename on disk where the file is |
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83 staged. This may differ from the resource name. If not provided, |
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84 `basename` must be computed from the last path part of `location` and made |
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85 available to expressions. |
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86 |
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87 The `secondaryFiles` property is a list of File or Directory objects that |
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88 must be staged in the same directory as the primary file. It is an error |
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89 for file names to be duplicated in `secondaryFiles`. |
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90 |
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91 The `size` property is the size in bytes of the File. It must be computed |
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92 from the resource and made available to expressions. The `checksum` field |
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93 contains a cryptographic hash of the file content for use it verifying file |
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94 contents. Implementations may, at user option, enable or disable |
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95 computation of the `checksum` field for performance or other reasons. |
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96 However, the ability to compute output checksums is required to pass the |
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97 CWL conformance test suite. |
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98 |
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99 When executing a CommandLineTool, the files and secondary files may be |
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100 staged to an arbitrary directory, but must use the value of `basename` for |
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101 the filename. The `path` property must be file path in the context of the |
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102 tool execution runtime (local to the compute node, or within the executing |
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103 container). All computed properties should be available to expressions. |
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104 File literals also must be staged and `path` must be set. |
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105 |
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106 When collecting CommandLineTool outputs, `glob` matching returns file paths |
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107 (with the `path` property) and the derived properties. This can all be |
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108 modified by `outputEval`. Alternately, if the file `cwl.output.json` is |
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109 present in the output, `outputBinding` is ignored. |
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110 |
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111 File objects in the output must provide either a `location` URI or a `path` |
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112 property in the context of the tool execution runtime (local to the compute |
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113 node, or within the executing container). |
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114 |
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115 When evaluating an ExpressionTool, file objects must be referenced via |
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116 `location` (the expression tool does not have access to files on disk so |
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117 `path` is meaningless) or as file literals. It is legal to return a file |
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118 object with an existing `location` but a different `basename`. The |
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119 `loadContents` field of ExpressionTool inputs behaves the same as on |
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120 CommandLineTool inputs, however it is not meaningful on the outputs. |
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121 |
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122 An ExpressionTool may forward file references from input to output by using |
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123 the same value for `location`. |
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124 |
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125 fields: |
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126 - name: class |
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127 type: |
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128 type: enum |
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129 name: File_class |
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130 symbols: |
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131 - cwl:File |
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132 jsonldPredicate: |
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133 _id: "@type" |
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134 _type: "@vocab" |
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135 doc: Must be `File` to indicate this object describes a file. |
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136 - name: location |
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137 type: string? |
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138 doc: | |
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139 An IRI that identifies the file resource. This may be a relative |
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140 reference, in which case it must be resolved using the base IRI of the |
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141 document. The location may refer to a local or remote resource; the |
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142 implementation must use the IRI to retrieve file content. If an |
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143 implementation is unable to retrieve the file content stored at a |
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144 remote resource (due to unsupported protocol, access denied, or other |
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145 issue) it must signal an error. |
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146 |
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147 If the `location` field is not provided, the `contents` field must be |
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148 provided. The implementation must assign a unique identifier for |
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149 the `location` field. |
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150 |
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151 If the `path` field is provided but the `location` field is not, an |
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152 implementation may assign the value of the `path` field to `location`, |
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153 then follow the rules above. |
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154 jsonldPredicate: |
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155 _id: "@id" |
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156 _type: "@id" |
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157 - name: path |
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158 type: string? |
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159 doc: | |
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160 The local host path where the File is available when a CommandLineTool is |
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161 executed. This field must be set by the implementation. The final |
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162 path component must match the value of `basename`. This field |
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163 must not be used in any other context. The command line tool being |
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164 executed must be able to to access the file at `path` using the POSIX |
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165 `open(2)` syscall. |
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166 |
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167 As a special case, if the `path` field is provided but the `location` |
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168 field is not, an implementation may assign the value of the `path` |
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169 field to `location`, and remove the `path` field. |
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170 |
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171 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) |
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172 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, |
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173 `<space>`, `<tab>`, and `<newline>`) or characters |
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174 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) |
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175 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) |
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176 then implementations may terminate the process with a |
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177 `permanentFailure`. |
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178 jsonldPredicate: |
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179 "_id": "cwl:path" |
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180 "_type": "@id" |
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181 - name: basename |
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182 type: string? |
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183 doc: | |
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184 The base name of the file, that is, the name of the file without any |
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185 leading directory path. The base name must not contain a slash `/`. |
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186 |
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187 If not provided, the implementation must set this field based on the |
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188 `location` field by taking the final path component after parsing |
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189 `location` as an IRI. If `basename` is provided, it is not required to |
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190 match the value from `location`. |
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191 |
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192 When this file is made available to a CommandLineTool, it must be named |
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193 with `basename`, i.e. the final component of the `path` field must match |
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194 `basename`. |
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195 jsonldPredicate: "cwl:basename" |
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196 - name: dirname |
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197 type: string? |
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198 doc: | |
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199 The name of the directory containing file, that is, the path leading up |
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200 to the final slash in the path such that `dirname + '/' + basename == |
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201 path`. |
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202 |
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203 The implementation must set this field based on the value of `path` |
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204 prior to evaluating parameter references or expressions in a |
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205 CommandLineTool document. This field must not be used in any other |
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206 context. |
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207 - name: nameroot |
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208 type: string? |
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209 doc: | |
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210 The basename root such that `nameroot + nameext == basename`, and |
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211 `nameext` is empty or begins with a period and contains at most one |
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212 period. For the purposess of path splitting leading periods on the |
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213 basename are ignored; a basename of `.cshrc` will have a nameroot of |
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214 `.cshrc`. |
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215 |
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216 The implementation must set this field automatically based on the value |
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217 of `basename` prior to evaluating parameter references or expressions. |
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218 - name: nameext |
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219 type: string? |
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220 doc: | |
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221 The basename extension such that `nameroot + nameext == basename`, and |
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222 `nameext` is empty or begins with a period and contains at most one |
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223 period. Leading periods on the basename are ignored; a basename of |
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224 `.cshrc` will have an empty `nameext`. |
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225 |
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226 The implementation must set this field automatically based on the value |
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227 of `basename` prior to evaluating parameter references or expressions. |
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228 - name: checksum |
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229 type: string? |
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230 doc: | |
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231 Optional hash code for validating file integrity. Currently must be in the form |
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232 "sha1$ + hexadecimal string" using the SHA-1 algorithm. |
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233 - name: size |
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234 type: long? |
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235 doc: Optional file size |
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236 - name: "secondaryFiles" |
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237 type: |
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238 - "null" |
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239 - type: array |
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240 items: [File, Directory] |
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241 jsonldPredicate: |
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242 _id: "cwl:secondaryFiles" |
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243 secondaryFilesDSL: true |
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244 doc: | |
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245 A list of additional files or directories that are associated with the |
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246 primary file and must be transferred alongside the primary file. |
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247 Examples include indexes of the primary file, or external references |
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248 which must be included when loading primary document. A file object |
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249 listed in `secondaryFiles` may itself include `secondaryFiles` for |
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250 which the same rules apply. |
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251 - name: format |
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252 type: string? |
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253 jsonldPredicate: |
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254 _id: cwl:format |
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255 _type: "@id" |
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256 identity: true |
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257 doc: | |
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258 The format of the file: this must be an IRI of a concept node that |
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259 represents the file format, preferrably defined within an ontology. |
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260 If no ontology is available, file formats may be tested by exact match. |
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261 |
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262 Reasoning about format compatability must be done by checking that an |
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263 input file format is the same, `owl:equivalentClass` or |
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264 `rdfs:subClassOf` the format required by the input parameter. |
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265 `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if |
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266 `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer |
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267 `<C> owl:subclassOf <A>`. |
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268 |
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269 File format ontologies may be provided in the "$schema" metadata at the |
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270 root of the document. If no ontologies are specified in `$schema`, the |
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271 runtime may perform exact file format matches. |
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272 - name: contents |
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273 type: string? |
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274 doc: | |
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275 File contents literal. Maximum of 64 KiB. |
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276 |
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277 If neither `location` nor `path` is provided, `contents` must be |
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278 non-null. The implementation must assign a unique identifier for the |
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279 `location` field. When the file is staged as input to CommandLineTool, |
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280 the value of `contents` must be written to a file. |
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281 |
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282 If `loadContents` of `inputBinding` or `outputBinding` is true and |
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283 `location` is valid, the implementation must read up to the first 64 |
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284 KiB of text from the file and place it in the "contents" field. |
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285 |
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286 |
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287 - name: Directory |
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288 type: record |
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289 docAfter: "#File" |
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290 doc: | |
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291 Represents a directory to present to a command line tool. |
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292 |
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293 Directories are represented as objects with `class` of `Directory`. Directory objects have |
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294 a number of properties that provide metadata about the directory. |
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295 |
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296 The `location` property of a Directory is a URI that uniquely identifies |
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297 the directory. Implementations must support the file:// URI scheme and may |
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298 support other schemes such as http://. Alternately to `location`, |
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299 implementations must also accept the `path` property on Directory, which |
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300 must be a filesystem path available on the same host as the CWL runner (for |
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301 inputs) or the runtime environment of a command line tool execution (for |
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302 command line tool outputs). |
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303 |
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304 A Directory object may have a `listing` field. This is a list of File and |
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305 Directory objects that are contained in the Directory. For each entry in |
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306 `listing`, the `basename` property defines the name of the File or |
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307 Subdirectory when staged to disk. If `listing` is not provided, the |
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308 implementation must have some way of fetching the Directory listing at |
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309 runtime based on the `location` field. |
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310 |
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311 If a Directory does not have `location`, it is a Directory literal. A |
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312 Directory literal must provide `listing`. Directory literals must be |
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313 created on disk at runtime as needed. |
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314 |
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315 The resources in a Directory literal do not need to have any implied |
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316 relationship in their `location`. For example, a Directory listing may |
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317 contain two files located on different hosts. It is the responsibility of |
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318 the runtime to ensure that those files are staged to disk appropriately. |
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319 Secondary files associated with files in `listing` must also be staged to |
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320 the same Directory. |
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321 |
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322 When executing a CommandLineTool, Directories must be recursively staged |
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323 first and have local values of `path` assigend. |
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324 |
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325 Directory objects in CommandLineTool output must provide either a |
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326 `location` URI or a `path` property in the context of the tool execution |
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327 runtime (local to the compute node, or within the executing container). |
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328 |
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329 An ExpressionTool may forward file references from input to output by using |
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330 the same value for `location`. |
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331 |
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332 Name conflicts (the same `basename` appearing multiple times in `listing` |
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333 or in any entry in `secondaryFiles` in the listing) is a fatal error. |
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334 |
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335 fields: |
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336 - name: class |
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337 type: |
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338 type: enum |
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339 name: Directory_class |
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340 symbols: |
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341 - cwl:Directory |
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342 jsonldPredicate: |
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343 _id: "@type" |
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344 _type: "@vocab" |
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345 doc: Must be `Directory` to indicate this object describes a Directory. |
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346 - name: location |
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347 type: string? |
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348 doc: | |
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349 An IRI that identifies the directory resource. This may be a relative |
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350 reference, in which case it must be resolved using the base IRI of the |
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351 document. The location may refer to a local or remote resource. If |
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352 the `listing` field is not set, the implementation must use the |
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353 location IRI to retrieve directory listing. If an implementation is |
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354 unable to retrieve the directory listing stored at a remote resource (due to |
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355 unsupported protocol, access denied, or other issue) it must signal an |
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356 error. |
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357 |
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358 If the `location` field is not provided, the `listing` field must be |
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359 provided. The implementation must assign a unique identifier for |
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360 the `location` field. |
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361 |
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362 If the `path` field is provided but the `location` field is not, an |
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363 implementation may assign the value of the `path` field to `location`, |
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364 then follow the rules above. |
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365 jsonldPredicate: |
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366 _id: "@id" |
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367 _type: "@id" |
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368 - name: path |
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369 type: string? |
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370 doc: | |
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371 The local path where the Directory is made available prior to executing a |
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372 CommandLineTool. This must be set by the implementation. This field |
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373 must not be used in any other context. The command line tool being |
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374 executed must be able to to access the directory at `path` using the POSIX |
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375 `opendir(2)` syscall. |
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376 |
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377 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) |
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378 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, |
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379 `<space>`, `<tab>`, and `<newline>`) or characters |
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380 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) |
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381 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) |
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382 then implementations may terminate the process with a |
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383 `permanentFailure`. |
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384 jsonldPredicate: |
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385 _id: "cwl:path" |
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386 _type: "@id" |
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387 - name: basename |
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388 type: string? |
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389 doc: | |
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390 The base name of the directory, that is, the name of the file without any |
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391 leading directory path. The base name must not contain a slash `/`. |
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392 |
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393 If not provided, the implementation must set this field based on the |
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394 `location` field by taking the final path component after parsing |
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395 `location` as an IRI. If `basename` is provided, it is not required to |
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396 match the value from `location`. |
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397 |
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398 When this file is made available to a CommandLineTool, it must be named |
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399 with `basename`, i.e. the final component of the `path` field must match |
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400 `basename`. |
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401 jsonldPredicate: "cwl:basename" |
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402 - name: listing |
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403 type: |
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404 - "null" |
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405 - type: array |
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406 items: [File, Directory] |
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407 doc: | |
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408 List of files or subdirectories contained in this directory. The name |
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409 of each file or subdirectory is determined by the `basename` field of |
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410 each `File` or `Directory` object. It is an error if a `File` shares a |
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411 `basename` with any other entry in `listing`. If two or more |
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412 `Directory` object share the same `basename`, this must be treated as |
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413 equivalent to a single subdirectory with the listings recursively |
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414 merged. |
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415 jsonldPredicate: |
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416 _id: "cwl:listing" |
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417 |
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418 - name: Labeled |
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419 type: record |
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420 abstract: true |
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421 fields: |
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422 - name: label |
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423 type: |
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424 - "null" |
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425 - string |
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426 jsonldPredicate: "rdfs:label" |
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427 doc: "A short, human-readable label of this object." |
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428 |
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429 |
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430 - name: Identified |
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431 type: record |
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432 abstract: true |
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433 fields: |
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434 - name: id |
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435 type: string? |
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436 jsonldPredicate: "@id" |
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437 doc: "The unique identifier for this object." |
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438 |
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439 |
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440 - name: LoadListingEnum |
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441 type: enum |
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442 symbols: [no_listing, shallow_listing, deep_listing] |
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443 doc: |
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444 - | |
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445 Specify the desired behavior for loading the `listing` field of |
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446 a Directory object for use by expressions. |
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447 - "no_listing: Do not load the directory listing." |
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448 - "shallow_listing: Only load the top level listing, do not recurse into subdirectories." |
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449 - "deep_listing: Load the directory listing and recursively load all subdirectories as well." |
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450 |
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451 |
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452 - name: LoadContents |
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453 type: record |
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454 abstract: true |
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455 fields: |
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456 - name: loadContents |
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457 type: boolean? |
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458 jsonldPredicate: "cwl:loadContents" |
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459 doc: | |
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460 Only valid when `type: File` or is an array of `items: File`. |
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461 |
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462 Read up to the first 64 KiB of text from the file and place it in the |
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463 "contents" field of the file object for use by expressions. |
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464 - name: loadListing |
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465 type: LoadListingEnum? |
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466 jsonldPredicate: "cwl:loadListing" |
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467 doc: | |
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468 Only valid when `type: Directory` or is an array of `items: Directory`. |
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469 |
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470 Specify the desired behavior for loading the `listing` field of |
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471 a Directory object for use by expressions. |
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472 |
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473 The order of precedence for loadListing is: |
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474 |
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475 1. `loadListing` on an individual parameter |
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476 2. Inherited from `LoadListingRequirement` |
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477 3. By default: `no_listing` |
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478 |
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479 - name: FieldBase |
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480 type: record |
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481 extends: Labeled |
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482 abstract: true |
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483 fields: |
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484 secondaryFiles: |
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485 type: |
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486 - "null" |
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487 - SecondaryFileSchema |
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488 - type: array |
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489 items: SecondaryFileSchema |
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490 jsonldPredicate: |
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491 _id: "cwl:secondaryFiles" |
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492 secondaryFilesDSL: true |
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493 doc: | |
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494 Only valid when `type: File` or is an array of `items: File`. |
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495 |
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496 Provides a pattern or expression specifying files or |
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497 directories that should be included alongside the primary |
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498 file. Secondary files may be required or optional. When not |
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499 explicitly specified, secondary files specified for `inputs` |
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500 are required and `outputs` are optional. An implementation |
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501 must include matching Files and Directories in the |
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502 `secondaryFiles` property of the primary file. These Files |
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503 and Directories must be transferred and staged alongside the |
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504 primary file. An implementation may fail workflow execution |
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505 if a required secondary file does not exist. |
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506 |
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507 If the value is an expression, the value of `self` in the expression |
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508 must be the primary input or output File object to which this binding |
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509 applies. The `basename`, `nameroot` and `nameext` fields must be |
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510 present in `self`. For `CommandLineTool` outputs the `path` field must |
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511 also be present. The expression must return a filename string relative |
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512 to the path to the primary File, a File or Directory object with either |
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513 `path` or `location` and `basename` fields set, or an array consisting |
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514 of strings or File or Directory objects. It is legal to reference an |
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515 unchanged File or Directory object taken from input as a secondaryFile. |
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516 The expression may return "null" in which case there is no secondaryFile |
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517 from that expression. |
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518 |
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519 To work on non-filename-preserving storage systems, portable tool |
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520 descriptions should avoid constructing new values from `location`, but |
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521 should construct relative references using `basename` or `nameroot` |
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522 instead. |
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523 |
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524 If a value in `secondaryFiles` is a string that is not an expression, |
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525 it specifies that the following pattern should be applied to the path |
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526 of the primary file to yield a filename relative to the primary File: |
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527 |
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528 1. If string ends with `?` character, remove the last `?` and mark |
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529 the resulting secondary file as optional. |
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530 2. If string begins with one or more caret `^` characters, for each |
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531 caret, remove the last file extension from the path (the last |
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532 period `.` and all following characters). If there are no file |
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533 extensions, the path is unchanged. |
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534 3. Append the remainder of the string to the end of the file path. |
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535 |
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536 streamable: |
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537 type: boolean? |
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538 doc: | |
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539 Only valid when `type: File` or is an array of `items: File`. |
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540 |
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541 A value of `true` indicates that the file is read or written |
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542 sequentially without seeking. An implementation may use this flag to |
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543 indicate whether it is valid to stream file contents using a named |
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544 pipe. Default: `false`. |
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545 |
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546 |
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547 - name: InputFormat |
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548 type: record |
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549 abstract: true |
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550 fields: |
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551 format: |
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552 type: |
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553 - "null" |
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554 - string |
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555 - type: array |
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|
556 items: string |
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557 - Expression |
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558 jsonldPredicate: |
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559 _id: cwl:format |
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560 _type: "@id" |
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561 identity: true |
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|
562 doc: | |
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563 Only valid when `type: File` or is an array of `items: File`. |
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564 |
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565 This must be one or more IRIs of concept nodes |
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566 that represents file formats which are allowed as input to this |
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567 parameter, preferrably defined within an ontology. If no ontology is |
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|
568 available, file formats may be tested by exact match. |
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|
569 |
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|
570 |
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571 - name: OutputFormat |
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572 type: record |
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|
573 abstract: true |
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|
574 fields: |
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|
575 format: |
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|
576 type: |
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|
577 - "null" |
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|
578 - string |
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579 - Expression |
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580 jsonldPredicate: |
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581 _id: cwl:format |
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582 _type: "@id" |
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583 identity: true |
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584 doc: | |
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585 Only valid when `type: File` or is an array of `items: File`. |
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586 |
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587 This is the file format that will be assigned to the output |
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588 File object. |
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589 |
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|
590 |
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591 - name: Parameter |
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592 type: record |
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593 extends: [FieldBase, sld:Documented, Identified] |
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594 abstract: true |
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595 doc: | |
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596 Define an input or output parameter to a process. |
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|
597 |
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|
598 |
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599 - type: enum |
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600 name: Expression |
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601 doc: | |
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602 'Expression' is not a real type. It indicates that a field must allow |
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603 runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement) |
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604 is declared and supported by the platform, the field must also allow |
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605 Javascript expressions. |
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|
606 symbols: |
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|
607 - cwl:ExpressionPlaceholder |
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|
608 |
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|
609 |
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610 - name: InputBinding |
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611 type: record |
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|
612 fields: |
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613 - name: loadContents |
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614 type: |
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|
615 - "null" |
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616 - boolean |
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617 jsonldPredicate: "cwl:loadContents" |
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|
618 doc: | |
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619 Use of `loadContents` in `InputBinding` is deprecated. |
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620 Preserved for v1.0 backwards compatability. Will be removed in |
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621 CWL v2.0. Use `InputParameter.loadContents` instead. |
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|
622 |
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|
623 Only valid when `type: File` or is an array of `items: File`. |
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|
624 |
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|
625 Read up to the first 64 KiB of text from the file and place it in the |
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|
626 "contents" field of the file object for use by expressions. |
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|
627 |
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|
628 |
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|
629 - name: IOSchema |
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|
630 extends: [Labeled, sld:Documented] |
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631 type: record |
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|
632 abstract: true |
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|
633 fields: |
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|
634 - name: name |
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|
635 type: string? |
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636 jsonldPredicate: "@id" |
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|
637 doc: "The identifier for this type" |
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|
638 |
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|
639 - name: InputSchema |
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|
640 extends: [IOSchema] |
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641 type: record |
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642 abstract: true |
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|
643 |
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|
644 - name: OutputSchema |
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645 extends: [IOSchema] |
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646 type: record |
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647 abstract: true |
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|
648 |
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|
649 |
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|
650 - name: InputRecordField |
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651 type: record |
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652 extends: [sld:RecordField, FieldBase, InputFormat, LoadContents] |
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|
653 specialize: |
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654 - specializeFrom: "sld:RecordSchema" |
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655 specializeTo: InputRecordSchema |
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|
656 - specializeFrom: "sld:EnumSchema" |
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657 specializeTo: InputEnumSchema |
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|
658 - specializeFrom: "sld:ArraySchema" |
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659 specializeTo: InputArraySchema |
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660 - specializeFrom: "sld:PrimitiveType" |
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661 specializeTo: CWLType |
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|
662 |
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|
663 |
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|
664 - name: InputRecordSchema |
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665 type: record |
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|
666 extends: ["sld:RecordSchema", InputSchema] |
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|
667 specialize: |
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|
668 - specializeFrom: "sld:RecordField" |
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669 specializeTo: InputRecordField |
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|
670 |
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|
671 |
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|
672 - name: InputEnumSchema |
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|
673 type: record |
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|
674 extends: ["sld:EnumSchema", InputSchema] |
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|
675 |
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changeset
|
676 |
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|
677 - name: InputArraySchema |
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|
678 type: record |
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|
679 extends: ["sld:ArraySchema", InputSchema] |
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|
680 specialize: |
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|
681 - specializeFrom: "sld:RecordSchema" |
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|
682 specializeTo: InputRecordSchema |
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|
683 - specializeFrom: "sld:EnumSchema" |
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|
684 specializeTo: InputEnumSchema |
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|
685 - specializeFrom: "sld:ArraySchema" |
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|
686 specializeTo: InputArraySchema |
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|
687 - specializeFrom: "sld:PrimitiveType" |
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|
688 specializeTo: CWLType |
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|
689 |
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changeset
|
690 |
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|
691 - name: OutputRecordField |
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|
692 type: record |
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|
693 extends: [sld:RecordField, FieldBase, OutputFormat] |
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|
694 specialize: |
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|
695 - specializeFrom: "sld:RecordSchema" |
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|
696 specializeTo: OutputRecordSchema |
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|
697 - specializeFrom: "sld:EnumSchema" |
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|
698 specializeTo: OutputEnumSchema |
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|
699 - specializeFrom: "sld:ArraySchema" |
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|
700 specializeTo: OutputArraySchema |
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|
701 - specializeFrom: "sld:PrimitiveType" |
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|
702 specializeTo: CWLType |
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|
703 |
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|
704 |
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|
705 - name: OutputRecordSchema |
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|
706 type: record |
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|
707 extends: ["sld:RecordSchema", "#OutputSchema"] |
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|
708 docParent: "#OutputParameter" |
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|
709 specialize: |
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|
710 - specializeFrom: "sld:RecordField" |
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|
711 specializeTo: OutputRecordField |
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|
712 |
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|
713 |
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|
714 - name: OutputEnumSchema |
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|
715 type: record |
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|
716 extends: ["sld:EnumSchema", OutputSchema] |
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|
717 docParent: "#OutputParameter" |
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|
718 |
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|
719 |
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|
720 - name: OutputArraySchema |
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|
721 type: record |
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|
722 extends: ["sld:ArraySchema", OutputSchema] |
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|
723 docParent: "#OutputParameter" |
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|
724 specialize: |
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|
725 - specializeFrom: "sld:RecordSchema" |
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|
726 specializeTo: OutputRecordSchema |
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|
727 - specializeFrom: "sld:EnumSchema" |
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|
728 specializeTo: OutputEnumSchema |
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|
729 - specializeFrom: "sld:ArraySchema" |
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|
730 specializeTo: OutputArraySchema |
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|
731 - specializeFrom: "sld:PrimitiveType" |
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|
732 specializeTo: CWLType |
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|
733 |
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|
734 |
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|
735 - name: InputParameter |
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|
736 type: record |
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|
737 abstract: true |
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|
738 extends: [Parameter, InputFormat, LoadContents] |
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|
739 fields: |
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|
740 - name: default |
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|
741 type: Any? |
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|
742 jsonldPredicate: |
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|
743 _id: sld:default |
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|
744 noLinkCheck: true |
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|
745 doc: | |
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|
746 The default value to use for this parameter if the parameter is missing |
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|
747 from the input object, or if the value of the parameter in the input |
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|
748 object is `null`. Default values are applied before evaluating expressions |
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|
749 (e.g. dependent `valueFrom` fields). |
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|
750 |
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|
751 |
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|
752 - name: OutputParameter |
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|
753 type: record |
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|
754 extends: [Parameter, OutputFormat] |
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|
755 abstract: true |
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|
756 |
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|
757 |
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|
758 - type: record |
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|
759 name: ProcessRequirement |
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|
760 abstract: true |
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|
761 doc: | |
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|
762 A process requirement declares a prerequisite that may or must be fulfilled |
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|
763 before executing a process. See [`Process.hints`](#process) and |
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|
764 [`Process.requirements`](#process). |
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|
765 |
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|
766 Process requirements are the primary mechanism for specifying extensions to |
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|
767 the CWL core specification. |
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|
768 |
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|
769 |
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|
770 - type: record |
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|
771 name: Process |
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|
772 extends: [Identified, Labeled, sld:Documented] |
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|
773 abstract: true |
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|
774 doc: | |
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|
775 |
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|
776 The base executable type in CWL is the `Process` object defined by the |
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|
777 document. Note that the `Process` object is abstract and cannot be |
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|
778 directly executed. |
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|
779 |
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|
780 fields: |
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|
781 - name: inputs |
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|
782 type: |
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|
783 type: array |
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|
784 items: InputParameter |
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|
785 jsonldPredicate: |
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|
786 _id: "cwl:inputs" |
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|
787 mapSubject: id |
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|
788 mapPredicate: type |
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789 doc: | |
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790 Defines the input parameters of the process. The process is ready to |
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791 run when all required input parameters are associated with concrete |
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792 values. Input parameters include a schema for each parameter which is |
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793 used to validate the input object. It may also be used to build a user |
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794 interface for constructing the input object. |
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795 |
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796 When accepting an input object, all input parameters must have a value. |
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797 If an input parameter is missing from the input object, it must be |
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798 assigned a value of `null` (or the value of `default` for that |
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799 parameter, if provided) for the purposes of validation and evaluation |
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800 of expressions. |
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801 |
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802 - name: outputs |
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803 type: |
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804 type: array |
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805 items: OutputParameter |
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806 jsonldPredicate: |
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807 _id: "cwl:outputs" |
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808 mapSubject: id |
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809 mapPredicate: type |
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810 doc: | |
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811 Defines the parameters representing the output of the process. May be |
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812 used to generate and/or validate the output object. |
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813 - name: requirements |
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814 type: ProcessRequirement[]? |
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815 jsonldPredicate: |
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816 _id: "cwl:requirements" |
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817 mapSubject: class |
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818 doc: | |
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819 Declares requirements that apply to either the runtime environment or the |
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820 workflow engine that must be met in order to execute this process. If |
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821 an implementation cannot satisfy all requirements, or a requirement is |
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822 listed which is not recognized by the implementation, it is a fatal |
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823 error and the implementation must not attempt to run the process, |
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824 unless overridden at user option. |
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825 - name: hints |
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826 type: Any[]? |
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827 doc: | |
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828 Declares hints applying to either the runtime environment or the |
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829 workflow engine that may be helpful in executing this process. It is |
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830 not an error if an implementation cannot satisfy all hints, however |
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831 the implementation may report a warning. |
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832 jsonldPredicate: |
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833 _id: cwl:hints |
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834 noLinkCheck: true |
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835 mapSubject: class |
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836 - name: cwlVersion |
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837 type: CWLVersion? |
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838 doc: | |
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839 CWL document version. Always required at the document root. Not |
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840 required for a Process embedded inside another Process. |
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841 jsonldPredicate: |
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842 "_id": "cwl:cwlVersion" |
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843 "_type": "@vocab" |
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844 |
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845 - name: InlineJavascriptRequirement |
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846 type: record |
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847 extends: ProcessRequirement |
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848 doc: | |
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849 Indicates that the workflow platform must support inline Javascript expressions. |
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850 If this requirement is not present, the workflow platform must not perform expression |
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851 interpolatation. |
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852 fields: |
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853 - name: class |
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854 type: string |
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855 doc: "Always 'InlineJavascriptRequirement'" |
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856 jsonldPredicate: |
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857 "_id": "@type" |
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858 "_type": "@vocab" |
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859 - name: expressionLib |
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860 type: string[]? |
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861 doc: | |
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862 Additional code fragments that will also be inserted |
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863 before executing the expression code. Allows for function definitions that may |
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864 be called from CWL expressions. |
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865 |
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866 |
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867 - name: CommandInputSchema |
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868 type: record |
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869 abstract: true |
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870 |
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871 - name: SchemaDefRequirement |
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872 type: record |
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873 extends: ProcessRequirement |
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874 doc: | |
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875 This field consists of an array of type definitions which must be used when |
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876 interpreting the `inputs` and `outputs` fields. When a `type` field |
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877 contain a IRI, the implementation must check if the type is defined in |
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878 `schemaDefs` and use that definition. If the type is not found in |
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879 `schemaDefs`, it is an error. The entries in `schemaDefs` must be |
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880 processed in the order listed such that later schema definitions may refer |
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881 to earlier schema definitions. |
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882 fields: |
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883 - name: class |
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884 type: string |
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885 doc: "Always 'SchemaDefRequirement'" |
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886 jsonldPredicate: |
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887 "_id": "@type" |
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888 "_type": "@vocab" |
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889 - name: types |
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890 type: |
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891 type: array |
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892 items: CommandInputSchema |
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893 doc: The list of type definitions. |
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894 |
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895 - name: SecondaryFileSchema |
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896 type: record |
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897 fields: |
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898 - name: pattern |
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899 type: |
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900 - string |
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901 - Expression |
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902 doc: | |
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903 Provides a pattern or expression specifying files or directories that |
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904 should be included alongside the primary file. |
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905 |
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906 If the value is an expression, the value of `self` in the expression |
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907 must be the primary input or output File object to which this binding |
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908 applies. The `basename`, `nameroot` and `nameext` fields must be |
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909 present in `self`. For `CommandLineTool` outputs the `path` field must |
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910 also be present. The expression must return a filename string relative |
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911 to the path to the primary File, a File or Directory object with either |
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912 `path` or `location` and `basename` fields set, or an array consisting |
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913 of strings or File or Directory objects. It is legal to reference an |
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914 unchanged File or Directory object taken from input as a secondaryFile. |
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915 The expression may return "null" in which case there is no secondaryFile |
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916 from that expression. |
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917 |
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918 To work on non-filename-preserving storage systems, portable tool |
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919 descriptions should avoid constructing new values from `location`, but |
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920 should construct relative references using `basename` or `nameroot` |
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921 instead. |
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922 |
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923 If a value in `secondaryFiles` is a string that is not an expression, |
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924 it specifies that the following pattern should be applied to the path |
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925 of the primary file to yield a filename relative to the primary File: |
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926 |
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927 1. If string ends with `?` character, remove the last `?` and mark |
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928 the resulting secondary file as optional. |
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929 2. If string begins with one or more caret `^` characters, for each |
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930 caret, remove the last file extension from the path (the last |
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931 period `.` and all following characters). If there are no file |
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932 extensions, the path is unchanged. |
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933 3. Append the remainder of the string to the end of the file path. |
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934 - name: required |
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935 type: ["null", boolean, string, Expression] |
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936 doc: | |
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937 An implementation must not fail workflow execution if `required` is |
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938 set to `false` and the expected secondary file does not exist. |
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939 Default value for `required` field is `true` for secondary files on |
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940 input and `false` for secondary files on output. |
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941 |
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942 - name: LoadListingRequirement |
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943 type: record |
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944 extends: ProcessRequirement |
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945 doc: | |
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946 Specify the desired behavior for loading the `listing` field of |
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947 a Directory object for use by expressions. |
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948 fields: |
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949 class: |
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950 type: string |
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951 doc: "Always 'LoadListingRequirement'" |
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952 jsonldPredicate: |
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953 "_id": "@type" |
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954 "_type": "@vocab" |
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955 loadListing: |
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956 type: LoadListingEnum? |
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957 jsonldPredicate: "cwl:loadListing" |