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devel:workflow_specification_syntax [2013/09/11 14:28] – [Example] epujadas | beewm:devel:workflow_specification_syntax [2016/05/20 12:11] (current) – admin | ||
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<code xml> | <code xml> | ||
- | < | + | < |
< | < | ||
< | < | ||
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< | < | ||
< | < | ||
- | <dataset name=" | + | <dataset name=" |
.... | .... | ||
</ | </ | ||
</ | </ | ||
< | < | ||
- | <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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< | < | ||
<dataset name=" | <dataset name=" | ||
- | <dataset name=" | + | <dataset name=" |
<dataset name=" | <dataset name=" | ||
</ | </ | ||
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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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When a process is started by submitting a particular workflow together with one or several input datasets, it will be checked that: | When a process is started by submitting a particular workflow together with one or several input datasets, it will be checked that: | ||
* the input dataset(s) identified by its storage ID exist in storage | * the input dataset(s) identified by its storage ID exist in storage | ||
- | * the input dataset(s) in storage have the same type as specified in the ''< | + | * the input dataset(s) in storage have the same type as specified in the ''< |
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==== <dataset type=" | ==== <dataset type=" | ||
- | Required. Corresponds to the dataset type provided by the storage. It is used for validation purposes. | + | Optional. Corresponds to the dataset type provided by the storage. It is used for validation purposes. |
==== <dataset stage=" | ==== <dataset stage=" | ||
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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: |
- | ==== 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="" | + | |
- | </ | + | |
- | </ | + | |
- | < | + | |
- | < | + | |
- | < | + | |
- | </ | + | |
- | + | ||
- | + | ||
- | The resolved workflow should be stored together with the stored results (as it is in the current iBrain2).\\ | + | |