From eb6fd4035fcda045b250e4a24574d23bee39b3a7 Mon Sep 17 00:00:00 2001
From: Ally Hawkins <ally.hawkins@ccdatalab.org>
Date: Mon, 5 Aug 2024 10:35:05 -0500
Subject: [PATCH] account for different hvg name in merged object

---
 merge.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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"