[LuLeom]

Describe your changes

Re-implements methods/combat in R with sva::ComBat, replacing the Python (scanpy) version.

The reason for the switch is that sva::ComBat supports ref.batch, so batches can be corrected towards a reference batch. The scanpy implementation can't do that.

Following the convention for parameterised methods introduced in #142, combat is implemented as a single component with a --target argument and two paramsets in info.variants:

• to_goal (--target goal): ref.batch = "1". Batch 1 is left unchanged and the other batches are corrected towards it.
• to_mid (--target mid, default): ref.batch = NULL. All batches are corrected towards the pooled mean (like the previous implementation).

As combat does not make use of specific control samples, I am using the prefix no_controls_.

Tested via:

• viash test src/methods/combat/config.vsh.yaml passes.
• A manual run viash run with --target goal.

Fixes #148

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!

[Copilot]

🟢 Approval recommended

No blocking issues were identified in correction logic, output handling, or parameterised workflow integration.

No open issues 🎉

What changed in this PR

Replaces Scanpy-based ComBat with R’s sva::ComBat, enabling reference-batch correction within the existing parameterised-method workflow.

Changes:

• Adds goal correction towards batch 1 and default mid correction across batches.
• Declares no-control variants and switches runtime dependencies to R.
• Documents the implementation change.

File	Description
src/​methods/​combat/​script.R	Implements correction targets and AnnData output.
src/​methods/​combat/​script.py	Removes the Scanpy implementation.
src/​methods/​combat/​config.vsh.yaml	Configures targets, variants, and R dependencies.
CHANGELOG.md	Records the ComBat implementation switch.

_{Review effort: Balanced}

[ghar1821]

LGTM!