From 2bc41eca1ebe514bc3f77069cbd3dc170bfc9c29 Mon Sep 17 00:00:00 2001 From: Blampey Quentin Date: Tue, 2 Apr 2024 23:21:28 +0200 Subject: [PATCH] add smk pipeline --- .github/workflows/ci.yml | 2 +- sopa/segmentation/aggregate.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 81545440..bbab9204 100644 --- 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 index 2fd56b13..3f02a82c 100644 --- 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):