Generate workflow from annotation diagram (analysis)

Analysis title

Generate workflow from annotation diagram

Provider

Biosoft

Class

GenerateWorkflow

Plugin

biouml.plugins.genomeenhancer (Genome Enhancer)

Description

This method generates and runs the Genome Enhancer workflow for multi-omics data processing based on the selected conditions: data categories from annotation diagram, studied diseases and tissue type from which the data was retrieved (optional parameter).

Additional parameters (expert options) of this method allow selection of certain steps of this analysis to be skipped:

If run workflow is selected, the generated workflow will be executed, otherwise, the method will create the workflow, but will not execute it.

If unique output is selected, the results of this method will be saved into a new folder (adding a consequent number to the name of the folder: (1), (2), etc, in case the folder with the same name already exists), otherwise the method will overwrite the results contained in the originally specified output folder.

If generate report is selected, the method will create a new Genome Enhancer report (Full story and Brief tale reports).

If notify when completed is selected, the method will send you an email once it will finish the analysis.

If add MTB report is selected, then MTB report will be generated. Please note that MTB report can be generated only for input genomics data and for not more than two conditions. If one of these rules is violated, the MTB report will not be generated.

Parameters:

• Data source – Data source.
• Species – Species.
• Tissue – Tissue.
• Diseases – Diseases.
• Choose your data for analysis – Choose your data for analysis
• Baseline (expert) – Use baseline if 2 and more conditions are selected
• Run workflow (expert) – Run workflow
• Unique output (expert) – Unique output
• Generate report (expert) – Generate report
• Notify when completed (expert) – Send e-mail notification when analysis is finished
• Add MTB report (expert) – Create Molecular Tumor Board report on genomics data if selected disease can be classified as cancer.
• Result path (expert) – Path to folder with results