diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
index e7014263..4f4c2483 100644
--- a/workflows/ampliseq.nf
+++ b/workflows/ampliseq.nf
@@ -873,7 +873,7 @@ workflow AMPLISEQ {
             ch_tree_for_robject = FASTA_NEWICK_EPANG_GAPPA.out.grafted_phylogeny.map { it = it[1] }.first()
         } else if (params.multiregion) {
             ch_tree_for_robject = SIDLE_WF.out.tree_nwk
-        } else if ( params.metadata && (!params.skip_alpha_rarefaction || !params.skip_diversity_indices) ) {
+        } else if ( run_qiime2 && params.metadata && (!params.skip_alpha_rarefaction || !params.skip_diversity_indices) ) {
             ch_tree_for_robject = QIIME2_DIVERSITY.out.tree_nwk
         } else {
             ch_tree_for_robject = []