QUAST_BINS can be very slow / Reconfigure BIN_SUMMARY table

Description of the bug

Creating issue as requested. This was over a year ago now but I had trouble with the QUAST_BINS process failing when running on very large numbers of bins.

My thought at the time was that this has something to do with the fact that it is implemented as a loop over each input FASTA file: https://github.com/nf-core/mag/blob/master/modules/local/quast_bins.nf, and that it's doing some kind of ORF calling for each bin.

edit: MetaQUAST calls genes using MetaGeneMark according to the paper: https://academic.oup.com/bioinformatics/article/32/7/1088/1743987

"In contrast with regular QUAST which uses GeneMarkS, MetaQUAST uses MetaGeneMark ([Zhu et al., 2010]) for gene prediction, which is developed specially for metagenomes."

edit 2:

The local module has --rna-finding --gene-finding set, so gene finding is turned on (this is disabled by default). A quick fix (ignoring SeqKit stuff) is to just remove these arguments - the pipeline profiles genes using Prodigal and Prokka anyway

Command used and terminal output

Relevant files

No response

System information

No response

Start by reading modules/local/quast_bins.nf, especially the --rna-finding and --gene-finding settings, and compare its behavior with the pipeline's Prodigal and Prokka profiling. Done should be demonstrated by a resolved QUAST_BINS or BIN_SUMMARY configuration that handles large numbers of bins without the reported failure or slowness.