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Make HVG identification more robust when low expression values are present #47

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Feb 20, 2024
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Make HVG identification more robust when low expression values are present #47

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19 changes: 15 additions & 4 deletions modules/identify_hvgs.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,21 @@ process IDENTIFY_HVGS {
import scanpy as sc

adata = sc.read_h5ad("${adata}")
sc.pp.highly_variable_genes(adata,
n_top_genes=${n_hvgs},
flavor="seurat_v3",
batch_key="batch")

span = 0.3 # default
worked = False

while not worked and span <= 1:
try:
sc.pp.highly_variable_genes(adata,
n_top_genes=10000,
flavor="seurat_v3",
span=span,
batch_key="batch")
worked = True
except:
span += 0.1
print(f"Increased span to {span}")

adata.var[["highly_variable"]].to_pickle("${meta.id}.hvgs.pkl")
"""
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