added force, delete_cache, and recover to baysor cli interface

Author: ctastad

cholab-prep/example_xenium-multichannel-config.yaml

@@ -39,6 +39,9 @@ segmentation:
     min_area: 30 # [optional] minimum area (in microns^2) for a cell to not be filtered
     prior_shapes_key: cell_id # [optional] if prior segmentation has been performed, this is the column in the transcript dataframe that indicated the cell that contains the transcript. This doesn't need to be provided if you run cellpose with Sopa.
     unassigned_value: UNASSIGNED # [optional] if prior segmentation has been performed and if 'cell_key' above is provided, this is the value given to transcript that is not contained inside any cell
+    force: true # [optional] if True, ignore failed patches and continue with the successful ones
+    delete_cache: true # [optional] whether to delete the cache after segmentation
+    recover: false # [optional] if True, recover the cache from a failed segmentation, and continue
     config: # [this is the baysor config, as in https://github.com/kharchenkolab/Baysor]
       data:
         exclude_genes: "NegControl*,BLANK_*,antisense_*,Blank*" # genes excluded from the Baysor segmentation

sopa/cli/segmentation.py

@@ -157,7 +157,11 @@ def _run_staining_segmentation(
     **method_kwargs: int,
 ):
     from sopa.io.standardize import read_zarr_standardized
-    from sopa.segmentation import StainingSegmentation, custom_staining_based, methods
+    from sopa.segmentation import (
+        StainingSegmentation,
+        custom_staining_based,
+        methods,
+    )
 
     from .utils import _default_boundary_dir
 
@@ -242,6 +246,9 @@ def baysor(
     ),
     min_area: float = typer.Option(default=0, help="Minimum area (in micron^2) for a cell to be considered as valid"),
     scale: float = typer.Option(default=None, help="Baysor scale parameter (for config inference)"),
+    force: bool = typer.Option(default=False, help="If True, ignore failed patches and continue with the successful ones."),
+    delete_cache: bool = typer.Option(default=True, help="Whether to delete the cache after segmentation."),
+    recover: bool = typer.Option(default=False, help="If True, recover the cache from a failed segmentation, and continue."),
 ):
     """Perform Baysor segmentation. This can be done on all patches directly, or on one individual patch."""
     import sys
@@ -253,7 +260,8 @@ def baysor(
     sdata = read_zarr_standardized(sdata_path)
 
     try:
-        baysor(sdata, config=config, min_area=min_area, patch_index=patch_index, scale=scale)
+        baysor(sdata, config=config, min_area=min_area, patch_index=patch_index, scale=scale, 
+               force=force, delete_cache=delete_cache, recover=recover)
     except CalledProcessError as e:
         sys.exit(e.returncode)
 

workflow/Snakefile

@@ -125,6 +125,7 @@ rule patch_segmentation_baysor:
     threads: 8
     params:
         baysor_config = args["segmentation"]["baysor"].as_cli(keys=["config"]),
+        baysor_params = args["segmentation"]["baysor"].as_cli(keys=["force", "delete_cache", "recover"]),
         sdata_path = paths.sdata_path,
     resources:
         cpus_per_task=8,
@@ -137,7 +138,7 @@ rule patch_segmentation_baysor:
             module purge
         fi
 
-        sopa segmentation baysor {params.sdata_path} --patch-index {wildcards.index} {params.baysor_config}
+        sopa segmentation baysor {params.sdata_path} --patch-index {wildcards.index} {params.baysor_config} {params.baysor_params}
         """
 
 rule patch_segmentation_comseg: