[FEATURE] bbmap/align control output better

[njohner]

Is your feature request related to a problem? Please describe

I'm using bbmap.sh to filter out host reads (paired-end or not) from metagenomics data. What I'd actually want is to keep only the unmapped reads, in one file if input is single end, and in two separate files otherwise (if possible as fastq.gz), as do other bbmap modules (bbduk or filterbyname).

Describe the solution you'd like

Being able to set the output format and whether we want a single file or not, as is done in filterbyname and being able to set whether we want all the reads, only the mapped or only the unmapped reads (i.e. set out, outm or outu for the output).

Describe alternatives you've considered

I could set outu and outu2 in process.ext.args but would need to use .bam extension to have the corresponding files returned and then I'd need to pick the correct files from the channel. Moreover I'd be writing a very large file with all the reads that I don't need...

Additional context

No response