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devel:workflow_specification_syntax [2013/09/11 14:49] – [task] epujadas | beewm:devel:workflow_specification_syntax [2016/05/17 16:17] – external edit 127.0.0.1 | ||
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<code xml> | <code xml> | ||
- | < | + | < |
< | < | ||
< | < | ||
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</ | </ | ||
< | < | ||
- | <module name=" | + | <module name=" |
<params (optional)> | <params (optional)> | ||
<param name=" | <param name=" | ||
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< | < | ||
< | < | ||
- | <dataset name=" | + | <dataset name=" |
<files (considered and required only for datasets to store) in_dir=" | <files (considered and required only for datasets to store) in_dir=" | ||
</ | </ | ||
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==== < | ==== < | ||
Name of the workflow. | Name of the workflow. | ||
+ | Workflow | ||
==== < | ==== < | ||
Author of the workflow. | Author of the workflow. | ||
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:!: This feature is not implemented. The application behaves as this value would be set to true. To be discussed if it is needed, since the directory of a dataset could be specified as metadata or as variable. | :!: This feature is not implemented. The application behaves as this value would be set to true. To be discussed if it is needed, since the directory of a dataset could be specified as metadata or as variable. | ||
+ | |||
+ | |||
+ | ==== <files in_dir=" | ||
+ | With this element, the files and/or directories to stage are selected. All the ''" | ||
+ | * located in the ''" | ||
+ | * matching the regex expression specified in the ''" | ||
===== <module name=" | ===== <module name=" | ||
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- | Bee supports the use of variables in its workflow description file. | + | Bee supports the use of variables in its workflow description file.\\ |
- | Variables are specified with the following terminology: | + | Variables are specified with the following terminology: |
- | ===== Variable types ===== | + | Please check **[[:beewm:devel:resolving_workflow_templates|Resolving Workflow Templates]]** for detailed information. |
- | ==== config ==== | + | |
- | The currently supported variable of this type is: | + | |
- | * **'' | + | |
- | The value corresponds to the property '' | + | |
- | The workflow template will be resolved by substituting this variable with the effectively used value to provide traceability.\\ | + | |
- | __Example__: | + | |
- | The template snippet: | + | |
- | <code xml> | + | |
- | < | + | |
- | </ | + | |
- | would be resolved into: | + | |
- | <code xml> | + | |
- | < | + | |
- | </ | + | |
- | + | ||
- | ==== task ==== | + | |
- | The currently supported variables of this type are: | + | |
- | | + | |
- | * **'' | + | |
- | This variables correspond the files where the cluster job (or task) standard output and standard error streams are directed.\\ | + | |
- | The extension of such files is defined to be: .**'' | + | |
- | These variables can be used in the task validations to specify the files to validate.\\ | + | |
- | These variables will not be resolved in the workflow template since in the case of parallel running modules, one set of such files is produced per task.\\ | + | |
- | In case there is interest on examining/ | + | |
- | __Example__:\\ | + | |
- | <code xml> | + | |
- | < | + | |
- | <dataset type=" | + | |
- | <files in_dir="" | + | |
- | <files in_dir="" | + | |
- | </ | + | |
- | </ | + | |
- | < | + | |
- | < | + | |
- | < | + | |
- | </ | + | |
- | + | ||
- | + | ||
- | ==== bee_indexer ==== | + | |
- | The currently supported variables of this type are: | + | |
- | | + | |
- | * **'' | + | |
- | These variables correspond, in parallel running modules, to the start and end indexes of the objects to analyze in one job (task).\\ | + | |
- | They can be used as arguments to be added to the executable in each of the parallel calls.\\ | + | |
- | The values of them will be calculated in each task, using the values specified as '' | + | |
- | These variables will not be resolved in the workflow template because they are used for parallel running modules, and therefore, one set of such values is produced per task.\\ | + | |
- | __Example__: | + | |
- | <code xml> | + | |
- | <module name=" | + | |
- | < | + | |
- | <param name=" | + | |
- | <param name=" | + | |
- | <param name=" | + | |
- | <param name=" | + | |
- | </ | + | |
- | < | + | |
- | < | + | |
- | < | + | |
- | <arg type=" | + | |
- | <arg type=" | + | |
- | <arg type=" | + | |
- | <arg type=" | + | |
- | <arg type=" | + | |
- | <arg type=" | + | |
- | <arg type=" | + | |
- | <arg type=" | + | |
- | </ | + | |
- | </ | + | |
- | </ | + | |
- | + | ||
- | + | ||
- | The resolved workflow should be stored together with the stored results (as it is in the current iBrain2).\\ | + | |