Hi everyone, Any help with the issue below (involving #CE9MS66BS and #C01U1E95JQ5) would be much appreciated: https://nfcore.slack.com/archives/C070369GP7T/p1735754871023769

Which version of #C01U1E95JQ5 are you using? We have anticipated this problem and I thought we had solved it by prefixing the contig name with the genome name, but I can't find the code right now. @Danilo Di Leo, can you help?

I was using the magmap commit that is referenced in the code block from the original message. Feel free to test it

Thanks. I'll be back as soon as I get in touch with @Danilo Di Leo who wrote/didn't write the code.

Hi! At the moment we only check the presence of duplicates in the contig files. The next step could be to change the header of the fasta files but at the time we wrote the

<http://check_duplicate.nf|check_duplicate.nf>

module (see https://github.com/nf-core/magmap/blob/dev/modules/local/check_duplicates.nf) we decided to let the user to take care of it since it might be a corner case. (we didn't have any issues from users so far)

Sorry, I'd be happy to help but I'm not much of a dev, unfortunately

I fully agree with you @Alexandru Mizeranschi, they should work together.

Adding in both pipelines is the ideal solution ultimately!

I created a GitHub issue here: https://github.com/nf-core/magmap/issues/97

Thanks. I thought @Danilo Di Leo also made one when we discussed this in the morning, but I can't find it now. In any case, what we discussed was to edit the fasta files only for genomes that have duplicate contig names. For these, Prokka will always be called even if the user provides a gff file to avoid having to edit this too which could be risky.