openproblems-bio · ghar1821 · Apr 8, 2026 · Apr 8, 2026 · Apr 8, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -75,6 +75,8 @@
 
 ## MAJOR CHANGES
 
+* Removed `methods/cytovi` from the benchmark. The implementation is preserved in the `add-cytovi-implementation` branch to be revisited in the near future (PR #124).
+
 * Updated file schema (PR #18): 
   * Add is_control obs to indicate whether a cell should be used as control when correcting batch effect.
   * Removed donor_id obs from unintegrated censored.

diff --git a/src/methods/cytovi/config.vsh.yaml b/src/methods/cytovi/config.vsh.yaml
diff --git a/src/methods/cytovi/script.py b/src/methods/cytovi/script.py
diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
@@ -107,7 +107,6 @@ dependencies:
   - name: methods/batchadjust_all_controls
   - name: methods/rpca_to_goal
   - name: methods/rpca_to_mid
-  # - name: methods/cytovi
   - name: metrics/emd
   - name: metrics/ratio_consistent_peaks
   - name: metrics/average_batch_r2

diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf
@@ -34,7 +34,6 @@ methods = [
   limma_remove_batch_effect,
   rpca_to_goal,
   rpca_to_mid,
-  // cytovi
 ]
 
 // construct list of metrics