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nf-core

Hi differentialabundance team, I'm hitting a bug in differentialabundance 2.0.0 when I pass multiple gene set files via `gene_sets_files` (comma-separated): the GSEA_GSEA task fails with exit code 1 during post-processing

I also have the problem with multiple gmt files. `gsea-cli` names its output folder by embedding every input file's basename, comma-and-space separated, e.g. `...[C3_TFT_Legacy, C8_Cell_Type_Signature, ...].Gsea.`. That embedded space breaks the unquoted `mv` glob above. I believe it is a bug in the module's cleanup script. It reproduces with any 2+ files

Thanks for the report. Could you test with the `fix/gsea-multi-gmt-mv` branch for me? Once you confirm the fix is good I'll PR it via the modules repo

Hi <@U03SLE7RBAS> I tested the branch. The gsea-cli command ran to completion fine, but the pipeline died in the cleanup due to modules/nf-core/gsea/gsea/main.nf line 67 `rmdir *.Gsea.*`  The error is following `rmdir: failed to remove 'Glc.vs.CT.in.P_test_diffab_gsea_multi_gmt.[h.all.v2025.1.Hs.symbols,.Gsea.1787732891043.rpt': Not a directory`  Probably the pattern is too broad. And I think there is one more - the branch doesn't fix the unquoted `rpt_label` word-splitting

Are you able to take my starting point and tweak yourself to a version that works by changing the code yourself? If you could PR to `nf-core/modules`, so much the better. It'll be the fastest way for you to get this fixed :slightly_smiling_face: