Merge pull request #783 from AlexsLemonade/allyhawkins/hvgs-merged-ob…

…ject Account for different HVG name in merged object
AlexsLemonade · Aug 5, 2024 · a746b37 · a746b37
2 parents d65fdee + eb6fd40
commit a746b37
Showing 1 changed file with 2 additions and 2 deletions.
diff --git 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"