...

In that case, the pipeline can be collapsed, to hide the steps that are (no longer) relevant. For example, once the single-cell RNA-seq data has been quantified, Single cell counts data node will be a new analysis start point, as the subsequent analyses will not focus on alignment, UMI deduplication etc. To start, right-click on the task node which should become a boundary (=end) of the collapsed portion of your pipeline and select Collapse tasks (Figure 19).

All the tasks on that layer will turn purple. Then left-click the task which should be the other boundary of the collapsed portion. The tasks that will be collapsed will turn green and a dialog will appear (Figure 19). In the example shown in Figure 19, the tasks between Trim tags and Quantify barcodes will be collapsed. Give the collapsed section a name (up to 30 characters) and select Save.

Downloading Data

Data associated with any data node can be downloaded using the  Download data link in the context sensitive menu (Figure 18). Compressed files will be downloaded to the local computer where the user is accessing the Partek Flow server. Note that bigger files (such as unaligned reads) would take longer to download. For guidance, a file size estimate is provided for each data node. These zipped files can easily be imported by the Partek^® Genomics Suite^® software.

...