diff --git a/Snakefile b/Snakefile
index e910ee81368b4fb4ef6d9f9fbfe18a618ae8764b..cfe71a74ef8fc5fb8a3723ca79e40e73d17796d6 100644
--- a/Snakefile
+++ b/Snakefile
@@ -27,10 +27,10 @@ rule align_and_count_2D:
 		template="template16_pad100-adj.tif",
 		labels="labels_bin2+100.tif"
 	output:
-		directory("{folder}/day{day}/BF_TRITC_aligned.zarr"),
+		zarr = directory("{folder}/day{day}/BF_TRITC_aligned.zarr"),
 		table = "{folder}/day{day}/table.csv"
 	shell:
-		"python align.py {input.data} {output} {input.concentrations} {input.template} {input.labels} {output.table} 0" 
+		"python align.py {input.data} {output.zarr} {input.concentrations} {input.template} {input.labels} {output.table} 0" 
 	
 
 rule get_sizes_nd2: