diff --git a/tools/snapatac2/macros.xml b/tools/snapatac2/macros.xml
index bfa9414deb5..095a1f512cf 100644
--- a/tools/snapatac2/macros.xml
+++ b/tools/snapatac2/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.5.3</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">23.0</token>
     <xml name="requirements">
         <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement>
diff --git a/tools/snapatac2/preprocessing.xml b/tools/snapatac2/preprocessing.xml
index ad80e865ebd..06dc4665c8a 100644
--- a/tools/snapatac2/preprocessing.xml
+++ b/tools/snapatac2/preprocessing.xml
@@ -91,7 +91,7 @@ sa.pp.add_tile_matrix(
 )
 
 #else if $method.method == 'pp.make_gene_matrix'
-sa.pp.make_gene_matrix(
+adata = sa.pp.make_gene_matrix(
     adata,
     gene_anno = '$method.gene_anno',
     chunk_size = $method.chunk_size,
@@ -464,7 +464,7 @@ sa.metrics.tsse(
                     <has_text_matching expression="count_frag_as_reads = True"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" location="https://zenodo.org/records/11260316/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
+            <output name="anndata_out" location="https://zenodo.org/records/12548681/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
         </test>
         <test expect_num_outputs="2">
             <!-- metrics.tsse -->