Fix Workflow Issues (#152)

tansey-lab · Nov 15, 2024 · 075204d · 075204d
1 parent 90649a9
commit 075204d
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/nextflow/modules/nf-core/sopa_resolve/main.nf b/nextflow/modules/nf-core/sopa_resolve/main.nf
@@ -9,7 +9,7 @@ process SOPA_RESOLVE {
     tuple val(meta), path(sopa_zarr), path(segments)
 
     output:
-    tuple val(meta), path("${sopa_zarr}/.sopa_cache/cellpose_boundaries_done"), emit: done_file
+    tuple val(meta), path("${sopa_zarr}/shapes/cellpose_boundaries/shapes.parquet"), emit: done_file
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/src/nuc2seg/cli/combine_segmentations.py b/src/nuc2seg/cli/combine_segmentations.py
@@ -18,7 +18,7 @@
     celltype_histogram,
     celltype_area_violin,
 )
-from nuc2seg.preprocessing import create_shapely_rectangle
+from nuc2seg.xenium import create_shapely_rectangle
 from nuc2seg.utils import get_tile_idx, generate_tiles
 
 logger = logging.getLogger(__name__)