Once a pipeline has been built in a project, it can be saved and re-used in other projects. The settings for each of the tasks will be saved, including the advanced settings. However, when running a saved pipeline, you may be prompted to specify additional settings (see Running a Pipeline). Furthermore, the task version is also saved. In very rare cases, a pipeline may include a version of a task that is no longer supported by Partek Flow. In this situation, the most recent version of the task will be applied to the data. For more information on task versions, see Task Management.

To save a pipeline:

1. Click the Make a pipeline link at the bottom of the screen under the Analyses tab (Figure 1)

Figure 1. Make a pipeline link shown underneath the task graph, under the Analyses tab of a project

1. In the dialog, name the pipeline and add an optional description (Figure 2). Make sure the Section name is set to ****Pipelines

Figure 2. Add a name and description of the new pipeline

1. Left-click the rectangular you wish to save as part of the pipeline from the task graph. Selected tasks will have a thick black outline (Figure 3)

Figure 3. Choose the tasks from the task graph that you wish to include as part of the saved pipeline by left-clicking the rectangular task nodes. In this example, all four tasks will be saved

1. Click the Make pipeline button (Figure 2). This saves the pipeline and the screen will return to the Analyses tab. To check if the pipeline has been saved, select the circular data node preceding the first task in the saved pipeline and it will appear in the context sensitive menu on the right under Pipelines (see ).

Note that it is not necessary to select all of the tasks from the task graph. It is possible to select a subset of the tasks, but the selected tasks must be consecutive (Figure 4).

Figure 4. A subset of the tasks from the task graph can be saved as part of a pipeline, but the chosen tasks must be consecutive (top panel). Non-consecutive tasks (bottom panel) cannot be saved as part of a pipeline

It is also possible to select multiple layers and include them in the saved pipeline (Figure 5). Different colored layers represent tasks that have been re-run, possibly with different settings. Thus, including multiple layers in the saved pipeline allows you to incorporate the testing of different task settings as part of the pipeline. For more information on layers, please see .

Figure 5. Tasks from multiple layers can be included in a pipeline

It is possible to save a pipeline with a single task re-run with different settings (multiple layers). This can be a useful way to keep track of different task settings used. An alternative approach is to use saved option sets for individual tasks. This make it easier to track different task settings, as option sets can be viewed on the Option set management page. See for more details.

To have a document showing all the steps in a pipeline, select one of the final data nodes (e.g. a Feature list node in Figure 3) and choose Data summary report. Details of each task in a pipeline will be shown on a single page, which can be saved as a PDF or HTML file. See for more details.

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

A pipeline is a series of tasks used to process and analyze genomic data. Pipelines are built and managed under the Analyses tab of any project in Partek Flow. Additional information on pipelines is given in the Creating and Analyzing a Project documentation and there is further guidance on how to build analysis pipelines for different kinds of data on the tutorials page.

The combination of circular data nodes and rectangular task nodes displayed under the Analyses tab are herein collectively referred to as the task graph.

This user guide will cover the following topics:

• Making a Pipeline

Pipelines can also imported and managed on the page.

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

Pre-built pipelines are available for download from the Partek website. Please note, we are continually updating and improving our collection of pre-built pipelines. If you have any suggestions for improving any of the pre-built pipelines or suggestions for additional pipelines, please contact Partek technical support ([email protected]). In addition, pipelines can be imported from your local machine.

From Hosted Pipelines

1. Click the Import a pipeline link at the bottom of the screen under the Analyses tab (Figure 1).

Figure 1. Import a pipeline link below the Analyses tab

1. Select Hosted pipelines at the top of the Import pipeline page (Figure 2). This will display all available pre-built pipelines hosted by Partek.

Figure 2. Pre-built pipelines that can be imported from the Partek website. To preview a pipeline to see more detail, click the pipeline image

1. Click the Import pipeline button next to the pipeline you wish to import (Figure 2). Alternatively, click Import all pipelines at the bottom of the page to import all pipelines displayed.

You will be redirected back to the Analyses tab. When you select a circular data node, the newly imported pipeline will be available in the Pipelines section in the menu on the right (see Running a Pipeline).

From My Computer

To import a .pipeline file from your local machine into Partek® Flow®:

1. Click the Import a pipeline link at the bottom of the screen under the Analyses tab (Figure 1)

2. By default, My computer is selected at the top of the Import pipeline page. Click the Choose file button (Figure 3)

3. Browse to the location of the .pipeline file on your local machine and select it for upload. The selected file name will be displayed next to the Choose pipeline button (Figure 3)

Figure 3. Importing a pipeline from your local machine

You will be redirected back to the Analyses tab. When you select a circular data node, the newly imported pipeline will be available in the Pipelines section in the menu on the right (see ).

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

Only the Partek Flow user that created or imported a pipeline and administrative users have the ability to delete a pipeline. The delete option is not available to non-administrative users that that did not create or import a particular pipeline. To delete a pipeline:

1. Click on a circular under the tab and expand the Pipelines section from the menu on the right. The will only display pipelines that can be applied to the data type of the selected data node

2. Click Delete pipeline () for the pipeline you want to delete (Figure 1)\

All pipelines are automatically made available to all users on the same Partek Flow instance, making it easy to share pipelines. It is also possible to download a pipeline as a backup and to share with others. All saved and imported pipelines are available for all users on a Partek Flow instance to download. To download a pipeline:

1. Click on a circular data node under the Analyses tab and expand the Pipelines section from the menu on the right. The context-sensitive menu will only display pipelines that can be applied to the data type of the selected data node

2. Click Download pipeline () for the pipeline you want to download (Figure 1)

3. Choose a file location on your local machine and pipeline will be saved as a .pipeline file

Figure 1. Download a pipeline

The .pipeline file can then be shared, e.g. via email or USB stick, for use on other Partek Flow instances. See .

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

It is possible to view an image of the full pipeline before running it. All saved and imported pipelines are available for all users on a Partek Flow instance to preview. To preview a pipeline:

1. Click on a circular data node under the Analyses tab and expand the Pipelines section from the menu on the right. The context-sensitive menu will only display pipelines that can be applied to the data type of the selected data node

2. Click Preview pipeline () for the pipeline you want to preview (Figure 1)

Figure 1. Preview a pipeline

An image of the pipeline will be displayed at the center of the screen (Figure 2). To close the image and return to the Analyses tab, click outside of the image.

Figure 2. Preview image of a pipeline

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

Saved and imported pipelines can be applied to different data sets in other projects. Prior to running a saved or imported pipeline, the data needs to be imported and the sample attribute need to be specified under the Data tab. Pipelines that include tasks requiring sample attributes (e.g. GSA or ANOVA) will not run unless the sample attributes have been specified beforehand. All saved and imported pipelines are available for all users on a Partek Flow instance to run. To run a pipeline:

1. Click on a circular data node under the Analyses tab and expand the Pipelines section from the menu on the right (Figure 1). The context-sensitive menu will only display pipelines that can be applied to the data type of the selected data node

Figure 1. Loading a pipeline. In this example, the context-sensitive menu is showing all pipelines that can be applied to Aligned reads

1. Click on the pipeline name from the menu. Note that hovering the mouse over the pipeline name will show the description (if one was added) in a pop-out balloon

2. If further settings need to be specified for any of the tasks, you will be redirected to a task-specific page. For example, if the chosen pipeline includes a STAR alignment task, you need to specify the species and STAR aligner index (Figure 2). Other tasks that require additional settings include Quantification to annotation model, Differential gene expression, Variant detection and others. For each task, specify the requested settings and click Next. Other task settings that were specified when the pipeline was saved (e.g. alignment parameters) will be applied automatically.

Figure 2. Additional settings may be requested for certain tasks when loading a pipeline. In this example, the STAR alignment task is requesting an index to align to

The additional settings requested for certain tasks allows for flexibility in how the pipelines are used. For example, a pipeline that was initially created from a project on human data can be reused on data from another species by specifying a different Assembly (Figure 2). Other examples include performing quantification using different annotation models and customizing statistical models for different study designs.

Once additional settings have been specified for each task, all tasks will be queued and the jobs will run sequentially (Figure 3). The status of queued tasks can be monitored under the . If you have set up email notifications (see ), you will receive an email when the pipeline finishes.

Figure 3. All tasks in the chosen pipeline have been queued

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.