<param name=“processing_name” value=“xxx” />
<class>xxx</class>
<module processing_name=“xxx”
through <module name=“xxx”
<module cluster_queue=“xxx”>
by <module required_runtime_minutes=“xxx”>
and /or <module required_memory_mb=“xxx”>
corresponding to the mappings in the system.config
:Examples:
cluster_queue="SHORT" ----> required_runtime_minutes="30" cluster_queue="LONG" ----> required_runtime_minutes="720"
<module version=“1.*.*” class=“ch.systemsx.bee.workflowmanager.module.ClusterModule”
<params>
and </params>
through <executable>
and </executable>
<param name=“command_script” value=“xxx”>
through <path>xxx</path>
<args>
element to contain the different <arg..>
elements.<param name=“argument_x”…>
through an equivalent <arg…>
element in the same sort order.Example:
<params> <param name="indexbuilder_dataset" value="hcs_plate" /> <param name="indexbuilder_regex" value=".*_cDAPI.*\.(TIF|JP2)$" /> <param name="indexes_per_job" value="400" /> <param name="indexes_start" value="2" /> </params>
<input from_module=“0”>
through workflow input datasets.Example:
<input from_module="0"> <resources> <resource name="hcs_plate" value="(^i)([^_]+)(_m)([^_]+)(_b)([^_]+)(_u)([^_]+)" /> </resources> </input> ----> <workflow> <input> <datasets> <dataset name="hcs_plate" id="${RawImages}" type="HCS_IMAGE_RAW" stage="true" /> </datasets> </input>...
<input from_module=“n”>
where n > 0, through an output dataset in the n-moduleExample:
<input from_module="1"> <resources> <resource name="cpv1_create_batch_file_output_directory" value="Cpv1BatchFile" /> </resources> </input> ----> <output> <datasets> <dataset name="Cpv1BatchFile" store="false" />...
<storage><dataset_type>
element through a corresponding <output><datasets><dataset>
element in the same module.Example:
<storage enabled="true"> <dataset_type name="CLUSTER_JOB_LOGS"> <files in_dir="" regex_pattern=".*\.STDERR$" out_dir="" /> <files in_dir="" regex_pattern=".*\.STDOUT$" out_dir="" /> </dataset_type> </storage> ----> <output> <datasets> <dataset type="CLUSTER_JOB_LOGS" store="true"> <files in_dir="" regex=".*\.stderr" /> <files in_dir="" regex=".*\.stdout" /> </dataset>
<output_checks mode=“task_level”>
through <validations level=“task”>,
and <output_checks mode=“module_level”>
through <validations level=“module”>
, and move them into the <output>
element, after the <datasets>
definition.<validations>
sections substitute:<validate>
by <validation>
resource_type=“xxx”
attributesresource_regex=“{IB2_STDOUT_LOG}”
by regex=“${task.log_stdout}”
resource_regex=“{IB2_STDERR_LOG}”
by regex=“${task.log_stderr}”
resource_regex=“xxx”
by regex=“xxx”
comparator=“is_equal_to”
by comparator=“equal”
comparator=“is_superior_to”
by comparator=“greater”
(other allowed comparators are: less, not_equal, greater_or_equal, less_or_equal)pattern_regex
by content_regex
fail_status=“VALIDATION_ERROR”
by fail_status=“validation_error”
fail_status=“VALIDATION_WARNING”
by fail_status=“validation_warning”
Please, check the details in the workflow.xml
specification syntax document: Workflow Template Specification