dada2_fun changes

• change amplicon argument to "cutadapt". set to TRUE and inform sequence primers to trim primers with cutadapt. add cutadapt step in singleend SOP (illumina/torrent).

• add extension argument to inform R1 R2 pattern for paired data

• fixes

• update wiki and usecase

https://forgemia.inra.fr/umrf/ranomaly/-/wikis/home#dada2-usage-according-to-raw-data-type