GitLab

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

Downplaying the number of threads needed for deepTools and overall cleaning of the threads usage in the pipe

Adding blacklist downloads and removal from bam files. Also removing non canonical chromosoms and how i get them

Adding a small comment to the new plot profile multiqc output, while I wait to see if I can manually edit names of already published modules.

Reusing the reference-point for computeMatrix_QC. MultiQC1.8 allows now the integration of plotProfile outpus in the report

Removing non canonical chromosoms to compute chromHMM states to ensure that we have a consistent number of output files. Save some file cluttering too

Removing some print test statement and cdommenting the one I use to see what are in the dictionaries. Adding a rulegraph

Modifyin the install dependencies to get some downloaded data in a new data folder. Also corrected some minor things on the trackhub part when testing the downloaded data

Correcting the makeUCSChub to match the new name of macs files. ALso using proper narrow broad peaks

Conflicts:
	snakefile.smk