From 7ed393706909cdb03d05325f925fef5da75ec2c6 Mon Sep 17 00:00:00 2001
From: Alec Wysoker <alecw@broadinstitute.org>
Date: Thu, 7 May 2026 17:36:36 -0400
Subject: [PATCH] Support matrix.mtx.gz cellbender remove-background input

cellbender remove-background can use as input the file triplet matrix.mtx.gz,
barcodes.tsv.gz, features.tsv.gz.  This change enables this input format via:
- passing the 3 files in the h5ad input parameter;
- and setting task.ext.input = '.', which tells remove-background to look for the
  3 files in the working directory.
---
 modules/nf-core/cellbender/removebackground/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/cellbender/removebackground/main.nf b/modules/nf-core/cellbender/removebackground/main.nf
index 4cd0d6d3c748..ee0b435a1793 100644
--- a/modules/nf-core/cellbender/removebackground/main.nf
+++ b/modules/nf-core/cellbender/removebackground/main.nf
@@ -30,13 +30,14 @@ process CELLBENDER_REMOVEBACKGROUND {
         prefix = task.ext.prefix ?: "${meta.id}"
         args = task.ext.args ?: ""
         use_gpu = task.ext.use_gpu ? "--cuda" : ""
+        input = task.ext.input ?: "${h5ad}"
         """
         TMPDIR=. cellbender remove-background \
             ${args} \
             --cpu-threads ${task.cpus} \
             --estimator-multiple-cpu \
             ${use_gpu} \
-            --input ${h5ad} \
+            --input ${input} \
             --output ${prefix}.h5
         """