Open svarona opened 5 months ago
In cutadapt module for primer sequence trimming, in de novo assembly subworkflow, primer sequences are given as -A and -a by default: https://github.com/nf-core/viralrecon/blob/3731dd3a32a67a2648ea22c2bd980c224abdaee2/modules/local/cutadapt.nf#L25
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.
ext.arg
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
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: https://github.com/nf-core/viralrecon/blob/3731dd3a32a67a2648ea22c2bd980c224abdaee2/modules/local/cutadapt.nf#L25
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