Issue #324 - Githubissues

PCA part of initial QC
DEG_ALL folder is created during initialQC for all sample reporting
All subread (gene/gene_junction/junction) output is reported to DEG_ALL
All sample RSEM output is reported to DEG_ALL
extra columns in contrasts.tab for cpm cutoff and minsamples (with this cutoff)
create "DEG< group1 >-< group2 > < cpmcutoff > < minsamples >" folders in the working folder
contrasts specific RSEM output (only groups in contrast) is reported in "DEG< group1 >-< group2 > < cpmcutoff > < minsamples >" ... it is preformated to integer from float.
DEG only performed for RSEM_genes for now
groups.tab is required to run initial qc ... this is not reflected in the GUI
same contrasts can be rerun with different cpm_cutoffs
old "DEG_*" folders are removed
groups.tab and contrasts.tab can be provided at the initial qc stage ... groups.tab is required
warning added for selecting the wrong genome ... ie GRCh38 can only be selected for scRNASeq pipeline
annotations for existing genomes updated
hs37d5 and hs38d1 added for RNASeq and ChIPSeq pipelines.
"Low abundance" stuff for CPM and minsamples cutoffs from the DEG gui frame have been removed (commented out)

CCBR / Pipeliner