Oktoberfest fails if spectra file contains more than one dot

[gritukan]

Hi!

Describe the bug

I had a spectra file with two dots (say, foo.bar.mzML) and Oktoberfest fails because cannot find some intermediate file.

https://pastebin.com/7HshTDTN -- log
https://pastebin.com/zsRimguE -- config

msms directory has 20250729_EX1_UM1_Potte005_SA_EXT00_3hDDA_SKNAS_ACN_03.rescore msms.prosit files while Oktoberfest is looking for 20250729_EX1_UM1_Potte005_SA_EXT00_3hDDA_SKNAS_ACN_03.trimmed.rescore.

Running the same pipeline but with _trimmed instead of .trimmed works fine.

To Reproduce

Steps to reproduce the behavior:

• Run oktoberfest with spectra file containing two or more dots.

Expected behavior

Pipeline does not fail

System [please complete the following information]:

Ubuntu 24.04.4 LTS, Python 3.12.3, oktoberfest==0.10.0