12801 bug in gsea module related with multiple gene sets processing - #12821
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12801 bug in gsea module related with multiple gene sets processing#12821brovolia wants to merge 4 commits into
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Ran this for real before going further — pulled the gsea-cli 4.3.2 container and ran the actual script against real GCT/CLS/CHIP data plus two split Hallmark GMT files.
- Comma-joined
-gmx file1.gmt,file2.gmt: succeeds, combines both files (Got gsets: 50), output dir is plain<rpt_label>.Gsea.<timestamp>— no bracketed name list. - Space-separated (what this module currently produces): also exits 0, but gsea-cli silently keeps only the first file and drops the rest (
to parse>hallmark_part1.gmt< got: [hallmark_part1.gmt]). No crash.
So the real bug is silent data loss, not a crash, and join(',') fixes it. Couldn't reproduce the crash or the bracketed-name naming issue — details inline.
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I added some changes that we've discussed. But still I believe that the pipeline-level changes should also take place, eg in |
…iple-gene-sets-processing
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I narrowed the removal pattern and used quotation marks, so the white space will not break the processes