the names of the output files for diffex contain now the name of the counting tool

Closes #6

See merge request !8

correct bug qui mettait une virgule à la fin de chaque ligne dans le fichier de comptage star_star

Closes #6

See merge request !7

Resolve "add htseq-count as counter"

Closes #5

See merge request !6

Integration of STAR as mapper.

Closes #4

See merge request !4

-remove todo

- modification of stringtie rules to use hisat2 output and star output
- add in config file the possibility to use the pipeline in one shot or in comparison mode

- fastq.gz should be uncompressed for star
- changer genomedir for star mapping

- 1 rule index
- 1 rule star_single
- 1 rule star_paired

add star in singularity

Resolve "manage single and paired"

Closes #3

See merge request !3

Resolve "snakecdysis integration"

Closes #2

See merge request !1