From f33e7ccea5988647cd9531a32f520940ab8e8a5c Mon Sep 17 00:00:00 2001
From: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Fri, 13 Dec 2024 17:01:35 +0100
Subject: [PATCH] Fix scVI workflow not passing the layer to the component.
 (#936)

* Fix scVI workflow not passing the layer to the component.

* Update CHANGELOG
---
 CHANGELOG.md                                  | 2 ++
 src/workflows/integration/scvi_leiden/main.nf | 3 ++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ad121add731..13d7f3900f3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -49,6 +49,8 @@
 
 ## BUG FIXES
 
+* `scvi_leiden` workflow: fix the input layer argument of the workflow not being passed to the scVI component (PR #936). 
+
 * `scgpt/embedding`: remove unused argument `dbsn` (PR #875).
 
 * `scgpt/binning`: update handling of empty rows in sparse matrices (PR #875).
diff --git a/src/workflows/integration/scvi_leiden/main.nf b/src/workflows/integration/scvi_leiden/main.nf
index dae586a19e8..185e02ac42a 100644
--- a/src/workflows/integration/scvi_leiden/main.nf
+++ b/src/workflows/integration/scvi_leiden/main.nf
@@ -24,7 +24,8 @@ workflow run_wf {
           "lr_factor": state.lr_factor,
           "lr_patience": state.lr_patience,
           "output_model": state.output_model,
-          "modality": state.modality
+          "modality": state.modality,
+          "input_layer": state.layer,
        ]
       },
     // use map when viash 0.7.6 is released