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By following the steps in this tutorial, you have built a pipeline. You can save this pipeline for future use.

Select Create new pipeline near the bottom left-hand side of the browser window
Select the Pre-alignment QA/QC, Trim bases, Align reads, Post-alignment QA/QC, Quantify to annotation model, Filter features, Normalize counts, PCA, and GSA task nodes to include them in the pipeline
Name the pipeline; we have chosen RNA-Seq basic analysis
Give a description for the pipeline; we have noted trim <20, STAR, normalize with total count and add 0.001, GSA
Select Create pipeline (Figure 1)

Flow Documentation > Saving and running a pipeline > Screenshot 2023-08-09 at 15.26.04.png

To access this pipeline in the future, select an unaligned reads data node and choose Pipelines from the task menu. Available saved pipelines will be available to choose from the Pipelines section of the task menu (Figure 2).

Flow Documentation > Saving and running a pipeline > Screenshot 2023-08-09 at 15.27.15.png

After selecting the pipeline, you will be prompted to choose the reference genome for alignment, the annotation for quantification, and the contrasts for GSA. After selecting these options, the pipeline will automatically run. See Pipelines for more information.