Hey guys, is there a reason that crisprseq using MAGeCK RRA does not allow for setting --paired ? Or did I just miss it

Hi, that in general it would be possible to add it, but that requires that the order of the sample is specified correctly in the mageck test command line, which I am not sure it is guaranteed by the way that the command line is constructed by the pipeline. If you are interested, you can open an issue (or even try to implement it). I was going to look into this anyway. Please consider that I have recently made major changes in the mageck test module (see PR #252). Hopefully, this will be merged to dev very soon.

Alright, good to know ! Ive already started hotfixing it locally so I could use the pipeline with more flexibility (--control-gene --control-sgrna --paired --normcounts-to-file etc.). Regarding paired, I was under the impression that the order in the contrast file would be retained? So far this assumption held up in my examples.

wiht PR #252 I introduced some significant changes to make the mageck count use sample names in the count file and to consequently map conditions from the contrast file to sample names in the mageck test command... I did not check carefully, but my educated guess is that after these changes the order of the samples in the command line comes from the order of the lines in the samplesheet. Anyway, I will try to look into this asap. In the meanwhile, if you are willing to contribute, feel free!

Right now finishing the analysis is the main priority. I will also wait until your changes are through and then I might contribute !