Cleanup of un-used temp files within RGI

[SamD28]

Description of feature

Hello,

I recently ran funcscan on a quite fragmented genome which resulted in alot of intermediate files - RGI produces ~4 files per contig which when it becomes very fragmented results in a huge number of small files.

There is an option within RGI to clean these tmp files which are un-used in the rest of funcscan

--clean    removes temporary files (default: False)

After speaking to James on slack I am suggesting we add this to

ext.args2  = [
            "--alignment_tool ${params.arg_rgi_alignmenttool}",
            "--data ${params.arg_rgi_data}",
            params.arg_rgi_includeloose ? '--include_loose' : '',
            params.arg_rgi_includenudge ? '--include_nudge' : '',
            params.arg_rgi_lowquality ? '--low_quality' : '',
            params.arg_rgi_split_prodigal_jobs ? '--split_prodigal_jobs' : '',
            "--clean",
        ].join(' ').trim()

so that by default these un-used files are removed

It would be even better to add this as a pipeline parameter to make this easier to control if you want to keep these files for any reason :)

Thanks,
Sam