add control on module, remove PAIRED from config, correct some bug, one rule for hisat2_map

See merge request !11

add image

Closes #6

See merge request !10

add logo, change config file, modify multiqc rule

See merge request !9

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