From e44772023421c31dec02d7679fd92be304ad8f47 Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Thu, 2 Jun 2022 14:02:56 +0200
Subject: [PATCH] upodate paths

---
 Snakefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Snakefile b/Snakefile
index e910ee8..cfe71a7 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:
-- 
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