Merge pull request #22 from khanlab/fix-nii

fix to use work ome-zarr as input for nifti conversion
khanlab · Apr 3, 2024 · df5008c · df5008c
2 parents 80448eb + f86927c
commit df5008c
Showing 1 changed file with 2 additions and 2 deletions.
diff --git 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),