linting

workflow/rules/common.smk

@@ -128,9 +128,11 @@ def get_bids_toplevel_targets():
     targets.append(bids_toplevel(resampled, "dataset_description.json"))
     return targets
 
+
 def dataset_is_remote(wildcards):
     return is_remote_gcs(Path(get_dataset_path(wildcards)))
 
+
 def get_input_dataset(wildcards):
     """returns path to extracted dataset or path to provided input folder"""
     dataset_path = Path(get_dataset_path(wildcards))
@@ -149,6 +151,7 @@ def get_input_dataset(wildcards):
     else:
         print(f"unsupported input: {dataset_path}")
 
+
 def get_metadata_json(wildcards):
     """returns path to metadata, extracted from local or gcs"""
     dataset_path = Path(get_dataset_path(wildcards))
@@ -158,7 +161,7 @@ def get_metadata_json(wildcards):
         return rules.blaze_to_metadata_gcs.output.metadata_json.format(**wildcards)
     else:
         return rules.blaze_to_metadata.output.metadata_json.format(**wildcards)
-        
+
 
 # import
 def cmd_extract_dataset(wildcards, input, output):

workflow/rules/import.smk

@@ -32,17 +32,18 @@ rule extract_dataset:
     shell:
         "{params.cmd}"
 
+
 rule blaze_to_metadata_gcs:
     input:
-        creds = os.path.expanduser(config["remote_creds"])
+        creds=os.path.expanduser(config["remote_creds"]),
     params:
         dataset_path=get_dataset_path_gs,
         in_tif_pattern=lambda wildcards: config["import_blaze"]["raw_tif_pattern"],
         storage_provider_settings=workflow.storage_provider_settings,
     output:
         metadata_json=bids(
             root=root,
-            desc='gcs',
+            desc="gcs",
             subject="{subject}",
             datatype="micr",
             sample="{sample}",
@@ -84,15 +85,17 @@ rule blaze_to_metadata:
             config["import_blaze"]["raw_tif_pattern"],
         ),
     output:
-        metadata_json=temp(bids(
-            root=work,
-            subject="{subject}",
-            desc='local',
-            datatype="micr",
-            sample="{sample}",
-            acq="{acq,[a-zA-Z0-9]*blaze[a-zA-Z0-9]*}",
-            suffix="SPIM.json",
-        )),
+        metadata_json=temp(
+            bids(
+                root=work,
+                subject="{subject}",
+                desc="local",
+                datatype="micr",
+                sample="{sample}",
+                acq="{acq,[a-zA-Z0-9]*blaze[a-zA-Z0-9]*}",
+                suffix="SPIM.json",
+            )
+        ),
     benchmark:
         bids(
             root="benchmarks",
@@ -121,7 +124,7 @@ rule blaze_to_metadata:
 
 rule copy_blaze_metadata:
     input:
-        json=get_metadata_json
+        json=get_metadata_json,
     output:
         metadata_json=bids(
             root=root,
@@ -131,7 +134,18 @@ rule copy_blaze_metadata:
             acq="{acq,[a-zA-Z0-9]*blaze[a-zA-Z0-9]*}",
             suffix="SPIM.json",
         ),
-    shell: 'cp {input} {output}'
+    log:
+        bids(
+            root="logs",
+            datatype="copy_blaze_metadata",
+            subject="{subject}",
+            sample="{sample}",
+            acq="{acq}",
+            suffix="log.txt",
+        ),
+    shell:
+        "cp {input} {output} &> {log}"
+
 
 rule prestitched_to_metadata:
     input:
@@ -228,17 +242,17 @@ rule tif_to_zarr:
     script:
         "../scripts/tif_to_zarr.py"
 
+
 rule tif_to_zarr_gcs:
     """ use dask to load tifs in parallel and write to zarr 
         output shape is (tiles,channels,z,y,x), with the 2d 
         images as the chunks"""
     input:
         metadata_json=rules.copy_blaze_metadata.output.metadata_json,
-        creds = os.path.expanduser(config["remote_creds"])
+        creds=os.path.expanduser(config["remote_creds"]),
     params:
         dataset_path=get_dataset_path_gs,
-        in_tif_pattern=lambda wildcards:
-            config["import_blaze"]["raw_tif_pattern"],
+        in_tif_pattern=lambda wildcards: config["import_blaze"]["raw_tif_pattern"],
         intensity_rescaling=config["import_blaze"]["intensity_rescaling"],
         storage_provider_settings=workflow.storage_provider_settings,
     output: