add smk pipeline

gustaveroussy · Apr 2, 2024 · 2bc41ec · 2bc41ec
1 parent 035ccb5
commit 2bc41ec
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -58,7 +58,7 @@ jobs:
       #----------------------------------------------
       - name: Install dependencies
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --extras "dev cellpose" --no-interaction
+        run: poetry install --extras "dev cellpose snakemake" --no-interaction
 
       #----------------------------------------------
       #              perform tasks

diff --git a/sopa/segmentation/aggregate.py b/sopa/segmentation/aggregate.py
@@ -103,7 +103,7 @@ def standardize_table(self):
 
         if self.sdata.table is not None and self.overwrite:
             del self.sdata.table
-        self.sdata.table = self.table
+        self.sdata.tables["table"] = self.table
         save_table(self.sdata)
 
     def filter_cells(self, where_filter: np.ndarray):