Merging Devel into Master with mostly RNASeq updates
Merging devel into master with mostly chenges in the RNA-Seq pipeline: In short:
- Added FC and FDR options for filtering DESeq2
- Added default genomes for FASTQSCREEN and summarised Fastqscreen visualisation in the report
- Bugfixes in the report for GO Term, insertsize
- Fixed extractions for STAR parameters
- Fixed parameter in the subread module
- TPM calculations for the DESeq2 module
- Updates of descriptions
- Cutadapt fixes
- Add ESSENTIAL_FRAGLEN for bamCoverage
- Improvements on the RNA-Seq report
- Improvements of the genebodycoverage plots within the report (samples displayed in one plot)