diff --git a/modules/identify_hvgs.nf b/modules/identify_hvgs.nf index bf693a8..7f201f2 100644 --- a/modules/identify_hvgs.nf +++ b/modules/identify_hvgs.nf @@ -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") """