From 2636991ba40fdca8e80d3361033a6f6285575160 Mon Sep 17 00:00:00 2001
From: Devika Agarwal <33758226+deevdevil88@users.noreply.github.com>
Date: Thu, 14 Nov 2024 17:06:07 +0000
Subject: [PATCH 1/3] Update integration  pipeline.yml to add run option for
 scib

---
 panpipes/panpipes/pipeline_integration/pipeline.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/panpipes/panpipes/pipeline_integration/pipeline.yml b/panpipes/panpipes/pipeline_integration/pipeline.yml
index a8693636..681bada6 100644
--- a/panpipes/panpipes/pipeline_integration/pipeline.yml
+++ b/panpipes/panpipes/pipeline_integration/pipeline.yml
@@ -250,6 +250,7 @@ plotqc:
 #-------------
 #Obs columns containing the cell type labels
 scib:
+  run: True
   rna:
   prot:
   atac:

From 83873623e091fe072e600c54adc286122ca72a51 Mon Sep 17 00:00:00 2001
From: Devika Agarwal <33758226+deevdevil88@users.noreply.github.com>
Date: Thu, 14 Nov 2024 17:13:06 +0000
Subject: [PATCH 2/3] Update pipeline_integration.py

added an active_if Run option for scib and LISI
---
 panpipes/panpipes/pipeline_integration.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/panpipes/panpipes/pipeline_integration.py b/panpipes/panpipes/pipeline_integration.py
index 916ff047..ee812384 100644
--- a/panpipes/panpipes/pipeline_integration.py
+++ b/panpipes/panpipes/pipeline_integration.py
@@ -817,6 +817,7 @@ def plot_umaps(infile, outfile):
 
 #this can follow now any mtd generation, but it will collate only RNA jobs for lisi
 @follows(collate_integration_outputs)
+@active_if(PARAMS['lisi_run'])
 @transform(collate_integration_outputs, 
            formatter(),  'logs/7_lisi.log')
 def run_lisi(infile, outfile):
@@ -834,6 +835,7 @@ def run_lisi(infile, outfile):
 
 
 @follows(collate_integration_outputs)
+@active_if(PARAMS['scib_run'])
 @transform(collate_integration_outputs, formatter(),  'logs/scib.log')
 def run_scib_metrics(infile, outfile):
     cell_mtd_file = sprefix + "_cell_mtd.csv"

From 9462f9c2e5dfa4bd392ba195414ceb38d2ebe087 Mon Sep 17 00:00:00 2001
From: Devika Agarwal <33758226+deevdevil88@users.noreply.github.com>
Date: Thu, 14 Nov 2024 17:15:01 +0000
Subject: [PATCH 3/3] Update  integration pipeline.yml

added `run` params for LISI and SCIB
---
 panpipes/panpipes/pipeline_integration/pipeline.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/panpipes/panpipes/pipeline_integration/pipeline.yml b/panpipes/panpipes/pipeline_integration/pipeline.yml
index 681bada6..15cdbb0d 100644
--- a/panpipes/panpipes/pipeline_integration/pipeline.yml
+++ b/panpipes/panpipes/pipeline_integration/pipeline.yml
@@ -244,6 +244,11 @@ plotqc:
   atac:
   multimodal: rna:total_counts
 
+#-------------
+# LISI metrics
+#-------------
+lisi:
+  run: True
 
 #-------------
 # scib metrics