Running test = true on Sumner requires rmats_pairs.txt

[angarb]

Problem

While running on Sumner, the pipeline fails if you set test = true and do not provide a rmats.pairs file. No such file: /projects/anczukow-lab/NGS_analysis/Trowbridge_collaboration/test2/rmats_pairs.txt As the point is to run this until Star, you should not need an rmats_pairs.txt file.

Solution

Remove the rmats_pairs requirement if test = true (it seems to work like this on the cloud).

Implementation

[angarb]

Error did not replicate. Closing issue.