StamLab/stampipes — pull request #15 by fwip (2014-11-07 01:16:14+00:00)
Title: Barcode tally

Okay, this seems to be a pretty straight-forward port of my external barcode tally script into $STAMPIPES.

### Quick notes:

* Using `qmake -j 40`; spawns a bunch of little jobs that run pretty quickly. About 70s for 16M reads (base unit of parallelism is the fastq file), so hopefully they don't dominate the cluster too much. Qmake generates one "overhead" task.
* Spits out `barcode_report.txt` in the flowcell directory - also puts the `barcode_tally.sh` processing script and version info there - should I move this to a subdirectory? (Thinking `/flowcell_scripts/` or similar).
* New section in `create_processing.py` for mandatory, flowcell-level scripts. Not 100% sure this is the right approach; we could instead stick them in `processing.json`?

I think the main thing I want to check before merging is to get your thoughts on the script placement, @akjohnson