From 3324a7873b3f85dc4dbe577eebe0f0d546363472 Mon Sep 17 00:00:00 2001
From: f641l <florian.heyl@dkfz-heidelberg.de>
Date: Fri, 2 Feb 2024 11:49:08 +0100
Subject: [PATCH] fix issue 299

---
 modules/local/mtx_to_seurat.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/mtx_to_seurat.nf b/modules/local/mtx_to_seurat.nf
index d83575a4..73e260d2 100644
--- a/modules/local/mtx_to_seurat.nf
+++ b/modules/local/mtx_to_seurat.nf
@@ -20,9 +20,9 @@ process MTX_TO_SEURAT {
     script:
     def aligner = params.aligner
     if (params.aligner in [ 'cellranger', 'cellrangerarc' ]) {
-        matrix   = "matrix.mtx.gz"
-        barcodes = "barcodes.tsv.gz"
-        features = "features.tsv.gz"
+        matrix   = "filtered_feature_bc_matrix/matrix.mtx.gz"
+        barcodes = "filtered_feature_bc_matrix/barcodes.tsv.gz"
+        features = "filtered_feature_bc_matrix/features.tsv.gz"
     } else if (params.aligner == "kallisto") {
         matrix   = "*count/counts_unfiltered/*.mtx"
         barcodes = "*count/counts_unfiltered/*.barcodes.txt"