Make cutadapt primer's position ext.arg

[svarona]

Description of feature

In cutadapt module for primer sequence trimming, in de novo assembly subworkflow, primer sequences are given as -A and -a by default:

viralrecon/modules/local/cutadapt.nf

Line 25 in 3731dd3

def paired = meta.single_end ? "-a file:adapters.sub.fa" : "-a file:adapters.sub.fa -A file:adapters.sub.fa"

It would be nice to set this as an ext.arg, so each one can decide if their primers are in the 3' (-a/-A) or 5' (-g/-G) of the reads.

This is done already in the nf-core's cutadapt module, so replacing the local module with the nf-core one's could fix it:
https://github.com/nf-core/modules/blob/master/modules/nf-core/cutadapt/main.nf