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Add Run option params LISI and SCIB metrics for pipeline_integration.py #321

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merged 3 commits into from
Nov 27, 2024
Merged

Add Run option params LISI and SCIB metrics for pipeline_integration.py #321

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2636991
Update integration pipeline.yml to add run option for scib
deevdevil88 Nov 14, 2024
8387362
Update pipeline_integration.py
deevdevil88 Nov 14, 2024
9462f9c
Update integration pipeline.yml
deevdevil88 Nov 14, 2024
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2 changes: 2 additions & 0 deletions panpipes/panpipes/pipeline_integration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand All @@ -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"
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6 changes: 6 additions & 0 deletions panpipes/panpipes/pipeline_integration/pipeline.yml
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Expand Up @@ -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:
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