Merge pull request #321 from DendrouLab/deevdevil88-patch-3

Add Run option params LISI and SCIB metrics for pipeline_integration.py
DendrouLab · Nov 27, 2024 · d32952e · d32952e
2 parents b3c3262 + 9462f9c
commit d32952e
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diff --git 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"

diff --git a/panpipes/panpipes/pipeline_integration/pipeline.yml b/panpipes/panpipes/pipeline_integration/pipeline.yml
@@ -244,12 +244,18 @@ plotqc:
   atac:
   multimodal: rna:total_counts
 
+#-------------
+# LISI metrics
+#-------------
+lisi:
+  run: True
 
 #-------------
 # scib metrics
 #-------------
 #Obs columns containing the cell type labels
 scib:
+  run: True
   rna:
   prot:
   atac: