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Declare normalization_id on file_test_mod2 - #30

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rcannood merged 2 commits into
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fix/declare-normalization-id-test-mod2
Jul 29, 2026
Merged

Declare normalization_id on file_test_mod2#30
rcannood merged 2 commits into
mainfrom
fix/declare-normalization-id-test-mod2

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Describe your changes

run_benchmark/main.nf extracts metadata from --input_test_mod2 and then does:

def rna_norm = state.dataset_uns_mod1.modality == "GEX"
  ? state.dataset_uns_mod1.normalization_id
  : state.dataset_uns_mod2.normalization_id

rna_norm decides which methods run on which dataset (the preferred_normalization filter), so in the swap direction the whole routing hangs off normalization_id in test_mod2. file_test_mod1.yaml declares that slot; file_test_mod2.yaml never did. It works today only because process_dataset happens to copy it onto both objects.

One-slot change to write down what we already depend on.

Part of a series of PRs coming out of a pre-run review of the benchmark.

Checklist before requesting a review

  • I have performed a self-review of my code

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Bug fixes
  • Proposed changes are described in the CHANGELOG.md

  • CI Tests succeed and look good!

run_benchmark reads dataset_uns_mod2.normalization_id off this file to
route methods to the right dataset, but only file_test_mod1 declared it.
@rcannood rcannood mentioned this pull request Jul 29, 2026
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@rcannood
rcannood merged commit 20586be into main Jul 29, 2026
@rcannood
rcannood deleted the fix/declare-normalization-id-test-mod2 branch July 29, 2026 13:29
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