Hello, does --bwa_min_score works for other aligners? If not, how should I change it for bowtie2?

Hi, I am afraid this option does not exists for other aligners, however you can provide any argument to a process via a

custom.config

adding to your nextflow command

-c custom.config

e.g.:

withName: 'BOWTIE2_ALIGN' {
    ext.args   = '--score-min L,0,-0.6'
}

The only thing is that you will need to also provide this in the

custom.config

as this will otherwise overwritten by the

ext.args

in the

custom.config