Also what are we doing about this PR: https://github.com/nf-core/modules/pull/9997 Basically we want to change the name of the folder generated from bwamem2 (and 1, and probably other genome indexing) to rename the folder. As currently if you run it on two different genomes it'll emit both sets of files into

bwamem2

. Previously:

stub:
    def prefix = task.ext.prefix ?: "${fasta}"    
    """
    mkdir bwamem2
    touch bwamem2/${prefix}.0123
    touch bwamem2/${prefix}.ann
    touch bwamem2/${prefix}.pac
    touch bwamem2/${prefix}.amb
    touch bwamem2/${prefix}.bwt.2bit.64

Current suggestion:

stub:    
    prefix = task.ext.prefix ?: meta.id ? "${meta.id}" : "${fasta.baseName}"
    def suffix = task.ext.suffix ?: "${fasta.baseName}"
    """
    mkdir ${prefix}
    touch ${prefix}/${suffix}.0123
    touch ${prefix}/${suffix}.ann
    touch ${prefix}/${suffix}.pac
    touch ${prefix}/${suffix}.amb
    touch ${prefix}/${suffix}.bwt.2bit.64

Basically we want to figure out how to name the two prefixes.

IMO: Ditch the suffix and make it a static string -

index

or something. Keep the prefix in the directory name and give it a name like

${prefix}.bwamem2/

, so that if it gets the name of the input fasta you can differentiate it

I don't like having

.bwamem2

in the folder name

Why not?

I feel it is unnecessary