issues with gprofiler2/gost

[suzannejin]

Have you checked the docs?

• [x] nf-core website: troubleshooting
• [x] nf-core modules documentation

Description of the bug

Several issues found for module gprofiler2/gost:

1. Inconcistency between using --organism mmusculus or not Running with --organism mmusculus vs running with --organism null --gmt_file gprofiler_full_mmusculus.ENSG.gmt (gmt obtained by downloading from their website) will return different results.
2. Fixing the database using set_base_url and then run gost on an archived database works locally but somehow gives error in the CI (https://github.com/nf-core/modules/actions/runs/13199316156/job/36850361811)
3. By default, the module will not use the gmt_file given by user, if organism is specified. Maybe it should be the other way around?

Other issues that makes testing the module using nf-test difficult: 4. Fixing the database using set_base_url and then run gost on an archived database is extremely slow even for test dataset (about 8 min vs 30s when using the updated database). Not sure why, but it could be related to how gost interact with old archives.

[famosab]

Are you planning to work on fixing these issues yourself? :)

[suzannejin]

@famosab Hello! I am currently busy with other issues, so welcome if anybody wants to work on this :)

[akaviaLab]

@suzannejin One comment about your first issue

1. Inconcistency between using --organism mmusculus or not Running with --organism mmusculus vs running with --organism null --gmt_file gprofiler_full_mmusculus.ENSG.gmt (gmt obtained by downloading from their website) will return different results.

When downloading the GMT file, they remove KEGG and Transfac (TF), due to licensing reasons. Are those the differences you are referring to? If you remove KEGG and TF from the list of the sources, is the result the same as the downloaded GMT file?