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akhanf committed Oct 4, 2024
1 parent edea152 commit 7b91969
Showing 1 changed file with 1 addition and 2 deletions.
3 changes: 1 addition & 2 deletions workflow/scripts/tif_to_zarr_gcs.py
Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,12 @@
from lib.dask_image import imread_pages
import gcsfs
import pyvips
from dask.distributed import Client, LocalCluster

gcsfs_opts={'project': snakemake.params.storage_provider_settings['gcs'].get_settings().project,
'token': snakemake.input.creds}
fs = gcsfs.GCSFileSystem(**gcsfs_opts)

cluster = LocalCluster(n_workers=snakemake.threads, threads_per_worker=1)
dask.config.set(scheduler='threads', num_workers=snakemake.threads)

def replace_square_brackets(pattern):
"""replace all [ and ] in the string (have to use
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