update the pipeline
Merge branch 'master' of https://github.com/SciLifeLab/scilifelab
add comments
add comments to GenerateComplexityPlots.sh
Merge pull request #396 from Galithil/caliper_qc_flags

Caliper qc flags
Merge pull request #395 from jun-wan/master

 
update htseq and complexity plots
Merge branch 'master' into fix_log
Need to make sure I don't lose anything