From e598b858452f74fc8d93276e56ef1400ccd6b2a2 Mon Sep 17 00:00:00 2001
From: Bonita van Waardenburg <bonita.vanwaardenburg@crg.eu>
Date: Wed, 4 Mar 2026 11:42:47 +0100
Subject: [PATCH] Added new parameter cellbender_extraargs for CellBender

---
 .gitignore                             | 1 +
 modules/local/tools/cellbender/main.nf | 3 ++-
 nextflow.config                        | 1 +
 3 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index bf0b7fd..4f2a291 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,4 @@ logs/*
 seperate_scripts/*
 conf/[0-9]*
 work/*
+*scale*
diff --git a/modules/local/tools/cellbender/main.nf b/modules/local/tools/cellbender/main.nf
index ea10c43..099e55f 100644
--- a/modules/local/tools/cellbender/main.nf
+++ b/modules/local/tools/cellbender/main.nf
@@ -32,6 +32,7 @@ process CELLBENDER {
         --output cellbender_output.h5 \\
         --epochs 150 \\
         --expected-cells ${meta.expected_cells} \\
-        --fpr 0.01
+        --fpr 0.01 \\
+        ${params.cellbender_extraargs ?: ''}
     """
 }
diff --git a/nextflow.config b/nextflow.config
index 7c20bd2..44ba681 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -73,6 +73,7 @@ params {
 
     // Filtering parameters
     perform_cellbender =    false
+    cellbender_extraargs =  null
 
     // Parameters for external pipelines
     splitpipe_installation = null