Overview

This ‘pipeline’ is much smaller in scope than a standard pipeline. It simply take bcl files, converts them into fastq files, and generates a read_pairs.tsv file describing the read pairs.

This is equivalent to the first step of the RNA-Seq pipeline, so the only reason to use this one is if you need to do bcl2fastq outside of the normal RNA-Seq protocol. For example, if you have already run the RNA-Seq pipeline on one set of data and now you are being asked to combine those data with another set. You may want to use this pipeline to convert the new data to fastq, at which point you can combine the runs and run them all through the RNA-Seq pipeline again.