BIOPZ-Katsantoni Maria authored 3 years ago and BIOPZ-Gypas Foivos committed 3 years ago

and are therefore not required in the rules.
- Snakefile
 star_rpm: --outWigNorm (default RPM was used)
 star_rpm: --outWigStrand (default Stranded was used)
 rename_star_rpm_for_alfa: orientation in params is redundant (Fixes #152)
- single_end.snakefile.smk
 map_genome_star: outFilterMismatchNoverLmax
 map_genome_star: outFilterScoreMinOverLread
 map_genome_star: outFilterMatchNminOverLread
 quantification_salmon: --writeUnmappedNames
- paired_end.snakefile.smk
  pe_map_genome_star: outFilterMismatchNoverLmax
  pe_map_genome_star: outFilterScoreMinOverLread
  pe_map_genome_star: outFilterMatchNminOverLread
  quantification_salmon: --writeUnmappedNames