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devel:workflow_specification_syntax [2013/09/16 10:41] – epujadasbeewm:devel:workflow_specification_syntax [2016/05/17 16:17] – external edit 127.0.0.1
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 <code xml> <code xml>
-<workflow name="String (required)" author="String (required)" cleanup="TRUE|FALSE (optional, defaults to TRUE)">+<workflow name="String (optional)" author="String (required)" cleanup="TRUE|FALSE (optional, defaults to TRUE)">
     <hosts>     <hosts>
         <run_on>CLUSTER_HOST|LOCAL_HOST (optional, defaults to CLUSTER_HOST)</run_on>         <run_on>CLUSTER_HOST|LOCAL_HOST (optional, defaults to CLUSTER_HOST)</run_on>
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     </input>     </input>
     <modules>     <modules>
-        <module name="String (required)" version="Regex pattern (required)" class="String (optional, defaults to ch.systemsx.bee.workflowmanager.module.MockModule)" required_runtime_minutes="Integer (optional)" required_memory_mb="Integer (optional)" >+        <module name="String (required)" version="Regex pattern (required)" class="String (optional, defaults to ch.systemsx.bee.workflowmanager.module.MockModule)" required_runtime_minutes="Integer (optional)" required_memory_mb="Integer (optional)" cpus_per_job="Integer (optional)">
             <params (optional)>             <params (optional)>
                 <param name="indexbuilder_dataset|indexbuilder_regex|indexes_per_job|indexes_start (required)" value="String (required)" />                 <param name="indexbuilder_dataset|indexbuilder_regex|indexes_per_job|indexes_start (required)" value="String (required)" />
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             <output>             <output>
                 <datasets (optional)>                 <datasets (optional)>
-                    <dataset name="String (required for datasets not to store, no default)" type="String (required for datasets to store, no default)" store="TRUE|FALSE (optional, defaults to FALSE)" relevant="TRUE|FALSE (optional, defaults to TRUE)">+                    <dataset name="String (required for datasets not to store, no default)" type="String (required for datasets to store, no default)" store="TRUE|FALSE (optional, defaults to FALSE)" relevant="TRUE|FALSE (optional, defaults to TRUE)" dropbox="String: the name of the dropbox that will be used for storing the dataset. Optional, if it's not specified the type will be used as dropbox name.">
                         <files (considered and required only for datasets to store) in_dir="String (optional, defaults to the root of the module's work directory)" regex="Regex pattern (required)" />                         <files (considered and required only for datasets to store) in_dir="String (optional, defaults to the root of the module's work directory)" regex="Regex pattern (required)" />
                     </dataset>                     </dataset>
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 ==== <workflow name="..." ... > ==== ==== <workflow name="..." ... > ====
 Name of the workflow. Name of the workflow.
 +Workflow
 ==== <workflow author="..." ... > ==== ==== <workflow author="..." ... > ====
 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="..." regex="..." /> ====
 +With this element, the files and/or directories to stage are selected. All the ''"files"'' elements defined in an output dataset will be evaluated. The files and/or directories selected will be the following:
 +  * located in the ''"in_dir"'', as a subdirectory of the module's work directory; or located directly in the module's work directory if the ''"in_dir"'' attribute is empty.
 +  * matching the regex expression specified in the ''"regex"'' attribute.
  
 ===== <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:  **''${variable_type.variable_name}''**.\\ Variables are specified with the following terminology:  **''${variable_type.variable_name}''**.\\
-Please check **[[devel:resolving_workflow_templates|Resolving Workflow Templates]]** for detailed information.+Please check **[[:beewm:devel:resolving_workflow_templates|Resolving Workflow Templates]]** for detailed information.
  
  
beewm/devel/workflow_specification_syntax.txt · Last modified: 2016/05/20 12:11 by admin

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