snakefmt, update container

config/config.yml

@@ -162,5 +162,5 @@ report:
 
 
 containers:
-  spimprep: 'docker://khanlab/spimprep-deps:imaris-deps'
+  spimprep: 'docker://khanlab/spimprep-deps:v0.1.1'
 

workflow/rules/common.smk

@@ -174,7 +174,7 @@ def get_input_sample(wildcards):
         # sample was a tar file, so point to the extracted folder
         return rules.extract_sample.output.ome_dir.format(**wildcards)
 
-    elif sample_path.suffixes[-1] == '.ims':
+    elif sample_path.suffixes[-1] == ".ims":
         return get_sample_path_remote(wildcards)
     else:
         print(f"unsupported input: {sample_path}")

workflow/rules/imaris.smk

@@ -35,21 +35,24 @@ rule imaris_to_metadata:
     script:
         "../scripts/imaris_to_metadata.py"
 
+
 rule imaris_channel_to_zarr:
     input:
         ims=get_input_sample,
     params:
         channel=lambda wildcards: get_stains(wildcards).index(wildcards.stain),
     output:
-        zarr=temp(bids(
-            root=work,
-            subject="{subject}",
-            datatype="micr",
-            sample="{sample}",
-            acq="{acq}",
-            stain="{stain}",
-            suffix="imaris.zarr.zip",
-        )),
+        zarr=temp(
+            bids(
+                root=work,
+                subject="{subject}",
+                datatype="micr",
+                sample="{sample}",
+                acq="{acq}",
+                stain="{stain}",
+                suffix="imaris.zarr.zip",
+            )
+        ),
     log:
         bids(
             root="logs",
@@ -68,22 +71,27 @@ rule imaris_channel_to_zarr:
     resources:
         runtime=360,
         mem_mb=1000,
-    shadow: 'minimal'
+    shadow:
+        "minimal"
     script:
         "../scripts/imaris_channel_to_zarr.py"
 
 
 rule imaris_to_ome_zarr:
     input:
-        zarr=lambda wildcards: expand(bids(
-            root=work,
-            subject="{subject}",
-            datatype="micr",
-            sample="{sample}",
-            acq="{acq}",
-            stain="{stain}",
-            suffix="imaris.zarr.zip",
-        ),stain=get_stains(wildcards),allow_missing=True),
+        zarr=lambda wildcards: expand(
+            bids(
+                root=work,
+                subject="{subject}",
+                datatype="micr",
+                sample="{sample}",
+                acq="{acq}",
+                stain="{stain}",
+                suffix="imaris.zarr.zip",
+            ),
+            stain=get_stains(wildcards),
+            allow_missing=True,
+        ),
         metadata_json=rules.prestitched_to_metadata.output.metadata_json,
     params:
         max_downsampling_layers=config["ome_zarr"]["max_downsampling_layers"],
@@ -112,8 +120,7 @@ rule imaris_to_ome_zarr:
     resources:
         runtime=360,
         mem_mb=config["total_mem_mb"],
-    shadow: 'minimal'
+    shadow:
+        "minimal"
     script:
         "../scripts/imaris_to_ome_zarr.py"
-
-

workflow/rules/ome_zarr.smk

@@ -89,7 +89,6 @@ rule tif_stacks_to_ome_zarr:
         "../scripts/tif_stacks_to_ome_zarr.py"
 
 
-
 rule ome_zarr_to_nii:
     input:
         **get_storage_creds(),
@@ -138,4 +137,3 @@ rule ome_zarr_to_nii:
         config["containers"]["spimprep"]
     script:
         "../scripts/ome_zarr_to_nii.py"
-