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This user guide will cover the following topics:

• Saving a custom option set
• Option set management page
• Adding an option set from the command line

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A Bowtie alignment task will be used as an example, but the steps are the same for any task that allows configuration of advanced settings.
Click Configure in the Advanced options section on the Task setup page (Figure 1). Image RemovedFigure 1:

In the task-specific Advanced options dialog, hover the cursor over the tool tip ( ) icon to get more information on each setting. Make the desired changes to the settings and click Save as new (Figure 2). Note that clicking Apply will implement the custom option set for the current task, but the option set will not be saved for use in other projects. Image RemovedFigure 2:

Name the new custom option set, add a description (optional) and click Save in the New option set dialog (Figure 3). Image RemovedFigure 3:

The saved option set will appear in the drop-down list in the Advanced options section on the Task setup page (Figure 4). All saved option sets are available to all of the users of the same Partek Flow instance.

Image RemovedFigure 4:  

Option Set Management Page

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Choose a task from the selector and all associated option sets will be shown in a table (Figure 5). Click the Preview ( ) icon in the Actions column to display the option set (Figure 6). Click the red cross ( ) icon in the Actions column to delete an option set. Note that only the Partek Flow user who created an option set and administrative Partek Flow users are able to delete an option set. Image RemovedFigure 5:

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Adding an Option Set from the Command Line

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On the Option set management page, click the green Add option set from command line button (Figure 5, above). In the Add option set dialog (Figure 7), choose a task from the Select task drop-down list and the version number (if applicable). Name the option set by typing into the Name option set box. Add a description of the option set by typing into the Option set description box (optional). Paste the command line from the clipboard into the command line box and click Save. Image RemovedFigure 7:

The command line will be parsed, validated and converted into a Partek Flow option set. The Command line parsing report will summarize the Command, Recognized parameters and Ignored parameters (Figure 8). Partek Flow will ignore parameters with a syntax error or parameters already dealt with by other components of the software (e.g. input/output file paths, performance optimization). Click OK to close the report. The option set will now appear on the Option set management page (Figure 5, above) and can be applied to projects (Figure 4, above). Image RemovedFigure 8:

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