automatically pull col names to be analyzed with BAGEL

[slsevilla]

Description of the bug

Currently pipeline requires the user to input the columns to be analyzed within BAGEL.

According to documentation the -c flag in BAGEL is for the -c [columns to test]. Numbering begins after the GENE column with 1 through N cols. The columns to be tested are dependent on the samplesheet input and will be inconsistent and difficult for the user to identify.

For FC -c flag is control columns (check to see how to handle more than one column)

For BF -c flag is treatment columns at the same time

REFERENCE: https://htmlpreview.github.io/?https://github.com/hart-lab/bagel/blob/master/BAGEL-v2-tutorial.html

Proposed Solution

Will need to change the -c flag from controls col to treatment cols depending on the input