correct variable names
separate out flowcell info by flowcell [ci skip]
move memory resource statements into snakemake resources [ci skip]
little bugfixes to demux rules [ci skip]
correct get_one_lane_from_flowcell in demux.rules [ci skip]
fix [ci skip]
update merge_one_per_sample to new file structure [ci skip]
new snakemake seems to require --directory . in cluster mode?? [ci skip]
tweak memory requests [ci skip]
change default lastal ref dir [ci skip]
dont parallelize depletion for now.. it gets unwieldy and inefficient when processing hundreds of samples [ci skip]
fixes to directory paths [ci skip]
clear up some rule ambiguities [ci skip]
no longer ambiguous [ci skip]
clear up one more ambiguity [ci skip]
Broad LSF needs -M explicitly given [ci skip]
new snakemake changes tmp dir [ci skip]
up the default jvm mem size for FilterSamReads
rework pipelines: hs_deplete on each sample of each lane of each flowcell.  merge per sample before assembly. move lastal filter to end of hs_deplete and prinseq to trinity step. make lastal operate on bams. more supporting code. no tests.
fixes and resources adjustments