search

dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system
https://dib-lab.github.io/elvers/
Other
28 stars 3 forks source link

[MRG] override deseq2 default contrasts #93

Closed bluegenes closed 5 years ago

bluegenes commented 5 years ago

Deseq2 has a parameter that is different than nearly all others: contrasts. Contrasts must be a dictionary (containing the names of the two conditions to compare). However, since the name of each contrast is up to the user (based on their data), we're not able to properly override the default values with dictionary updates.

This change checks if the user has added any additional contrasts, and if so, sets our default contrasts to {}. This allows us to keep the default contrast information in the deseq2_params.yaml file both for 1. enabling easy test data runs, and 2. providing an example of what the contrasts info should look like.

thanks to @ACharbonneau for running into this bug

bluegenes commented 5 years ago

@ctb this solves the deseq2 contrast issue you discuss in #108 / #109 - ready for review and comments!