re-add the regional pairwise distances program to the standard proces…

…sing pipeline; related to #416
gerlichlab · Jan 31, 2025 · 8bbd253 · 8bbd253
1 parent 0bc2700
commit 8bbd253
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Showing 2 changed files with 7 additions and 6 deletions.
diff --git a/bin/cli/run_processing_pipeline.py b/bin/cli/run_processing_pipeline.py
@@ -570,12 +570,12 @@ def stages(self) -> list[pypiper.Stage]:
                 func=compute_locus_pairwise_distances, 
                 f_kwargs=rounds_params,
             ),
-            # pypiper.Stage(
-            #     name="pairwise_distances__regional", 
-            #     func=compute_region_pairwise_distances, 
-            #     f_kwargs=rounds_params,
-            #     nofail=True,
-            # ),
+            pypiper.Stage(
+                name="pairwise_distances__regional", 
+                func=compute_region_pairwise_distances, 
+                f_kwargs=rounds_params,
+                nofail=True,
+            ),
             pypiper.Stage(
                 name="locus_specific_spots_visualisation_data_prep", 
                 func=prep_locus_specific_spots_visualisation, 

diff --git a/docs/pipeline-execution-control-and-rerun.md b/docs/pipeline-execution-control-and-rerun.md
@@ -77,6 +77,7 @@ Below are the sequential pipeline stage names.
 * tracing_QC
 * spot_counts_visualisation__locus_specific
 * pairwise_distances__locus_specific
+* pairwise_distances__regional
 * locus_specific_spots_visualisation_data_prep
 * locus_spot_viewing_prep
 * cross_channel_signal_analysis