Information about Pipeline Outputs #3
Description
Hello,
First off, I wanted to compliment whoever wrote the documentation for your pipeline. If all bioinformatics software instructions were this clear, our work would be 1000% easier!
So... I was in the process of installing the pipeline on an AWS parallel cluster set up with Slurm like an HPC cluster but got stalled when I reached the Klue step since its repo is currently private (as I later found out from issue #1).
Before spending more time trying to get the pipeline working, I was wondering if you could describe the outputs of the pipeline. In my case, I am trying to obtain sample-specific (i.e. demultiplexed) FASTQs from a set of sublibraries (1 pair of FASTQs per sublibrary), each containing reads from all samples. Is that something that this pipeline outputs at any point?
If it's not already obvious, I'm very new to this type of data and don't have access to the proprietary Parse computational pipeline, which is why I'm trying to find alternative solutions.
If your pipeline doesn't output sample-specific reads and/or you know of a way to obtain that data, I'd love to get your input. Any help is highly appreciated!