Je-demultiplex output in workflows

Hi, I’m trying to use the output of the Je-demultiplex tool as the input for bowtie2 as part of a workflow. However, The way Je-demultiplex seems to handles its outputs is that it writes a hidden dataset with unassigned reads as well as a dataset containing the actual assigned reads. The next tool (bowtie2) only receives the unassigned read dataset and I cannot actually process my assigned reads. Does anybody know how to deal with this, or recommend a different demultiplexing tool that I can easily integrate in to a workflow (i.e., have a specific demultiplexed dataset be processed in a next step)?

Thanks!

hey, make sure you select the option “Output forward and reverse reads in dataset collections”. This should allow you to connect the output(s) to bowtie2. If you don’t want to map the unassigned reads, you can use the “apply rule to collection” tool to filter out the ‘unassigned’ dataset from the collection(s).