# Option Set Management

Partek Flow allows you to configure advanced settings for various tasks including adapter trimming (Cutadapt), alignment (various aligners), quantification (Cufflinks), differential gene expression analysis (GSA, ANOVA and Cuffdiff), variant detection (Partek, samtools and Freebayes) and variant annotation (SNPEff). User-defined option sets can be saved and applied to other projects.

This user guide will cover the following topics:

* [Saving a Custom Option Set](#saving-a-custom-option-set)
* [Option Set Management Page](#option-set-management-page)
* [Adding an Option Set from the Command Line](#adding-an-option-set-from-the-command-line)

## Saving a Custom Option Set

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).

![Figure 1. Access to advanced options page through the Configure link. The example shown is on a Task setup page of a Bowtie alignment](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-45f5a57139c4f9799e9ebc169f3984bbf2a86ffd%2Fbowtie-task-set-up.png?alt=media)

In the task-specific *Advanced options* dialog, hover the cursor over the **tool tip** (![information\_icon](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-a884bb0d29a3431e1108909f8dfd1d94bc48ee8e%2Fquestion_mark_info.png?alt=media)) 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.

![Figure 2. Advanced options for Bowtie alignment task. The tool tip describes the setting in a pop-out balloon. In this example, the seed length has been changed from the default 28 to 10](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-840605b639fff00c5cbd88fdfdce94f228ce14cf%2Fbowtie-advanced-options-dialog%20\(1\).png?alt=media)

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

![Figure 3. Name and describe the new custom option set](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-abb198781ad640f5e59cda9ee57e7d3648635600%2Fnew-option-set.png?alt=media)

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.

![Figure 4. To apply a saved option set, choose it from the drop-down list in the Advanced options section of the Task setup page](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-707edc8a0f91fe41450af333a15dae4615cc45f1%2Fshow-saved-option.png?alt=media)

## Option Set Management Page

To access the *Option set management* page, click the avatar in the top right corner, choose **Settings** and click **Option sets** under Components section on the left (Figure 5). This page can be accessed by administrative and non administrative Partek Flow users.

Choose a task from the selector and all associated option sets will be shown in a table (Figure 5). Click the three dots in the *Actions* column and select **View parameters** to display the option set (Figure 6). Select **Delete option set** 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.

![Figure 5. Option set management page displaying a Bowtie task option set](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-78ad19abc3de7da2ecc06a97173d5a0f18542a5d%2Foption-sets-page.png?alt=media)

![Figure 6. View an option set](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-f509765c6a4283a72d28c555d427a43a829ba1ba%2Fview-option-parameters.png?alt=media)

## Adding an Option Set from the Command Line

This is a Partek Flow licensed feature separate from the base license.

User-defined command lines can be copied and pasted to create a custom option set. This is particularly useful if, for example, you have previously run an alignment with custom options on the command line and wish to use the same set of options for an alignment in Partek Flow.

On the *Option set management* page, click the **+ Add option set from command line** button (Figure 5). 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 O*ption set name* 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**.

![Figure 7. Add option set dialog](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-18096701c85d2ec38db0ca4297a5fbfdd62b181f%2Fadd-command-line-option-set.png?alt=media)

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) and can be applied to projects (Figure 4).

![Figure 8. Command line parsing report](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-297d565315923d2c4cb278f0d4e36d821b15db54%2Fcommand-line-parsing-report.png?alt=media)

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.