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Merging Devel into Master with mostly RNASeq updates

Kreim, Nastasja requested to merge devel into master

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)

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