Allow readNamePattern via config for demulti and filt rules

cnobles / iGUIDE

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.

https://iguide.readthedocs.io/en/latest/

GNU General Public License v3.0

20 stars 9 forks source link

Allow readNamePattern via config for demulti and filt rules #44

Closed ressy closed 5 years ago

ressy commented 5 years ago

This supplies a custom readNamePattern for the demulti and filt rules via the configuration, if one is present. (If not, that argument is left out of the command line strings so nothing changes.) I'm using this change to process reads that have the SRA's weird naming. Fixes #43.

ressy commented 5 years ago

(Re-triggered the test with an empty commit since bioconda mysteriously gave a bunch of 404 errors the first time)

cnobles commented 5 years ago

Closing in favor of #50, which incorporates the current changes in master and extends the functionality to coupling portion of rules.