Add IRFinder to list workflows

[tbrittoborges]

IRFinder can be found here https://github.com/williamritchie/IRFinder

[tbrittoborges]

How to integrate IR information to the duj?

[boehmv]

I have some experience running IRFinder, although I found it not as straight-forward as leafcutter for example. The cool thing is that in the end it is basically the same as DESeq2 (it is used for the statistical tests), just the first steps are different. So maybe we could implement it as a separate "module", next to something like DESeq2?

I know it probably does not help you much, but I drag&dropped the files/codes I used for running IRFinder/DESeq2. I don't know whether this works or if there are better ways to share files? Also, please don't shame me for my amateur programming, it is a very basic and not very flexible script :)

Short explanation:
I have a bash script that defines folders, files, etc. called "Complete_Analysis_Template_paired_V002.sh". This basically runs through STAR, Salmon, DESeq2, ISAR, leafcutter and IRFinder. The IRFinder part starts around lines 489-583.

https://github.com/boehmv/RNAseq/blob/master/Complete_Analysis_Template_paired_V002.sh

There I basically iterate over the BAM files to sort them NOT by coordinate (lines 506-525) and subsequently run IRFinder (527-538).

Then I run DESeq2 on the IRFinder output files, partly by using an R script ("IRFinder.R")

https://github.com/boehmv/RNAseq/blob/master/IRFinder.R

Afterwards I run a python script to combine the IRFinder/DESeq2 output and generate an excel file:

https://github.com/boehmv/RNAseq/blob/master/xlsx_combine_IRFinder.py

Don't know whether all of this helps, it is probably much harder to implement this into the Baltica workflow, since it rather uses snakemake and so on?