[cemilcansaylan]

PR Checklist

• This comment contains a description of changes (with reason)
• Referenced issue is linked (none known, add if there is one)
• If you've fixed a bug or added code that should be tested, add tests! (custom_input is tested; the two new flags are not yet)
• Documentation in docs is updated

Description of changes
This fixes issue #400 and adds an optional rescoring run. Changes are following:

1. search_results_type: "custom_input": search results that are already in the internal Oktoberfest format can be used again. The file is only loaded, with no search engine conversion.
2. perform_rescoring (default true): when false, "run_rescoring" still preprocesses, calibrates, calculates features, and writes the merged inputs, but does not run Percolator/mokapot. Plotting and quantification are skipped with it, since they need the rescoring output. For DIA, the FDR control step is also skipped.
   3.perform_plotting (default true): when false, rescoring runs, but the summary plots are not generated.

Technical details

• custom_input is handled in pp.convert_search by returning pp.load_search(input_path), so runner._preprocess has no extra branching.
• The loaded file is used as is: no modification conversion, no PTM permutation, and nothing is written to msms/msms.prosit.

[codecov]

Codecov Report

❌ Patch coverage is 25.00000% with 18 lines in your changes missing coverage. Please review.
✅ Project coverage is 48.77%. Comparing base (4035b7c) to head (7e51026).
⚠️ Report is 1 commits behind head on hackathon_retreat_2026.

Files with missing lines	Patch %	Lines
oktoberfest/runner.py	0.00%	16 Missing ⚠️
oktoberfest/utils/config.py	66.66%	2 Missing ⚠️

Additional details and impacted files

@@                    Coverage Diff                     @@
##           hackathon_retreat_2026     #406      +/-   ##
==========================================================
- Coverage                   48.78%   48.77%   -0.01%     
==========================================================
  Files                          26       26              
  Lines                        3036     3053      +17     
  Branches                      438      442       +4     
==========================================================
+ Hits                         1481     1489       +8     
- Misses                       1479     1488       +9     
  Partials                       76       76              

Flag	Coverage Δ
unit-tests	48.77% <25.00%> (-0.01%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
oktoberfest/preprocessing/preprocessing.py	31.77% <100.00%> (+1.13%)	⬆️
oktoberfest/utils/config.py	80.53% <66.66%> (-0.19%)	⬇️
oktoberfest/runner.py	36.91% <0.00%> (-0.38%)	⬇️

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