Migrate from DSL1 to DSL2

[TheoC35]

I have made the necessary changes to migrate to DSL2.

Main changes :

• There is now a workflow in main.nf, as required in DSL2.
• filter has been renamed to filter_sam, as the previous name was conflicting with one of Nextflow's functions.

Minor changes :

• Parts of main.nf were using the deprecated DSL1 syntax and are now updated to DSL2. Most modifications are related to channels, input and output handling in processes.

Unless there is a bug, the behavior of ribomethseq-nf should be unaffected by this update.