Snakefile: defines where the samples lie, how the files are named, etc.
snakemakerules.STARrules.singleEnd: holds the most general rules for this
config.json: specifies for each rule how much computational power it gets on the cluster
countMatrix_standalone.R: called by the rule that produces a single countmatrix for all cells
run pipeline with: snakemake -p -j 80 --cluster-config /home/wertek/scripts/snakemake/config.json --cluster 'qsub -l walltime={cluster.time},mem={cluster.mem},nodes=1:ppn={cluster.threads}'