GitLab

Proper handling of SEACR QC. Still some errors due to SEACR removal of temp files. Snakemake just need to be rerun

ine working version of the pipeline, with still peak_calling being tough to parametrize for CUT&RUN

No more errors. Still weird peaks calling results, due to perhaps difficulty for macs to estimate fragment length with CUT&RUn data

Updating the multibigwig command to focus on chr1 to cut computing time. Also removing useless grouping per samples, since all deptools plots are now in the multiQC

Commenting cutrunsamples since not used yet and adding some check if there is no control at all in the samples

Working version of the pipeline, properly handling different peak calling strategies based on paired/single end data

Remaking call peaks to handle both samples that are paire end and with or whitout control, sugina mi of input fonctions and params magic to alter the command line provided in the shell. Lots of things to do still

Adding CUTRUN and PROPER CONTROl dict. No obvious errors before correcting some helerp functions and wildcards functions

Adding a grouped correlation plot for multiQC and adding the individual samples plots to the target rules