diff --git a/merge.nf b/merge.nf index c36819fc..c3c2bdac 100644 --- a/merge.nf +++ b/merge.nf @@ -109,8 +109,8 @@ process export_anndata { ${has_adt ? "--feature_name adt" : ''} # move normalized counts to X in AnnData - reformat_anndata.py --anndata_file ${rna_h5ad_file} - ${has_adt ? "reformat_anndata.py --anndata_file ${feature_h5ad_file}" : ''} + reformat_anndata.py --anndata_file ${rna_h5ad_file} --hvg_name "merged_highly_variable_genes" + ${has_adt ? "reformat_anndata.py --anndata_file ${feature_h5ad_file} --hvg_name 'none' " : ''} """ stub: rna_h5ad_file = "${merge_group_id}_merged_rna.h5ad"