From f86927c2a8b896c03322f3bd8759c67ba28a18ee Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Wed, 3 Apr 2024 11:45:40 -0400
Subject: [PATCH] fix to use work ome-zarr as input for nifti conversion

---
 workflow/rules/ome_zarr.smk | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflow/rules/ome_zarr.smk b/workflow/rules/ome_zarr.smk
index 6a7810c..76c0f55 100644
--- a/workflow/rules/ome_zarr.smk
+++ b/workflow/rules/ome_zarr.smk
@@ -84,12 +84,12 @@ rule ome_zarr_to_zipstore:
 rule ome_zarr_to_nii:
     input:
         zarr=bids(
-            root=root,
+            root=work,
             subject="{subject}",
             datatype="micr",
             sample="{sample}",
             acq="{acq}",
-            suffix="SPIM.ome.zarr.zip",
+            suffix="SPIM.ome.zarr",
         ),
     params:
         channel_index=lambda wildcards: get_stains(wildcards).index(wildcards.stain),