bam files from align PE reads empty about stacks_workflow

[enormandeau]

I did not adapt this workflow to use paired-end data yet, although I had started to work on it a while back. I always use single-end data only, both denovo and with a reference.

I intend to complete this at some point but it does not work for now. I'll update the script folders with a sub-folder named something like paired-end_not_working and add a note to the documentation in the README.md file too.

If you want to use paired-end data, please follow the info on the official STACKS website. You can always come back to stacks_workflow for its cutting edge filtration steps.

Sorry for the inconvenience.

[enormandeau]

The above changes were implemented.