Add option to export BAM file with reads aligned against the contigs to results folder

[alexhbnr]

Description of feature

Currently, nf-core/mag will keep the BAM files that resulted from aligning the short-read data against the assembled contigs using BowTie2 in the temporary work directory. However, for some subsequent analyses it might be helpful to keep these files for later. Therefore, an option to save these files into the results directory would be great.

[d4straub]

That should be possible via a config already. Thats tedious of course. If thats a more regular task then I agree to add a parameter to save bowtie bam files on request in the results folder.

[jfy133]

I can imagine this being a regular task, and is a simple enough change to add this IMO