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