cleanup and fixes

config/config.yml

@@ -5,8 +5,6 @@ work: 'work'
 
 remote_creds: '~/.config/gcloud/application_default_credentials.json' #this is needed so we can pass creds to container
 
-write_ome_zarr_direct: True #use this to skip writing the final zarr output to work first and copying afterwards -- useful when work is not a fast local disk
-
 use_zipstore: False #if True, produce SPIM.ome.zarr.zip instead of SPIM.ome.zarr
 
 #total resources available, used to set rule resources
@@ -47,7 +45,7 @@ bigstitcher:
     min_r: 0.7
     max_shift_total: 50
   global_optimization:
-    enabled: 1 
+    enabled: 1
     method: TWO_ROUND_ITERATIVE
     methods: #unused, only for reference
       ONE_ROUND_SIMPLE: "One-Round"

pyproject.toml

@@ -30,11 +30,11 @@ tifffile = "^2024.5.10"
 
 [tool.poe.tasks]
 test_localin_gcsout = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_local.tsv root='gcs://khanlab-lightsheet/data/test_bids'"
-test_localin_localout = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_gcs.tsv root=bids"
+test_localin_localout = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_local.tsv root=bids"
 test_gcsin_gcsout = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_gcs.tsv root='gcs://khanlab-lightsheet/data/test_bids'"
 test_gcsin_localout = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_gcs.tsv root=bids"
-test_localin_localout_zipstore = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_gcs.tsv root=bids use_zipstore=True"
-test_localin_gcsout_zipstore = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_gcs.tsv root='gcs://khanlab-lightsheet/data/test_bids' use_zipstore=True"
+test_localin_localout_zipstore = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_local.tsv root=bids use_zipstore=True"
+test_localin_gcsout_zipstore = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_local.tsv root='gcs://khanlab-lightsheet/data/test_bids' use_zipstore=True"
 
 [build-system]
 requires = ["poetry-core"]

workflow/rules/common.smk

@@ -183,7 +183,6 @@ def get_input_dataset(wildcards):
 def get_metadata_json(wildcards):
     """returns path to metadata, extracted from local or gcs"""
     dataset_path = Path(get_dataset_path(wildcards))
-    suffix = dataset_path.suffix
 
     if is_remote_gcs(dataset_path):
         return rules.blaze_to_metadata_gcs.output.metadata_json.format(**wildcards)

workflow/rules/import.smk

@@ -42,7 +42,7 @@ rule blaze_to_metadata_gcs:
         storage_provider_settings=workflow.storage_provider_settings,
     output:
         metadata_json=bids(
-            root=root,
+            root=work,
             desc="gcs",
             subject="{subject}",
             datatype="micr",