diff --git a/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl b/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl
index 89258cfe1..0af33b228 100644
--- a/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl
+++ b/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl
@@ -150,21 +150,32 @@ workflow scaffold_and_refine_multitaxa {
             "sample":              '{"entityType":"sample","entityName":"' + sample_id + '"}'
         }
 
-        scatter(h in assembly_header) {
-            String stat_by_taxon = stats_by_taxon[h]
+        if(assembly_length_unambiguous > min_scaffold_unambig) {
+            scatter(h in assembly_header) {
+                String stat_by_taxon = stats_by_taxon[h]
+            }
         }
     }
 
     ### summary stats
-    call utils.concatenate {
-      input:
-        infiles     = [write_tsv([assembly_header]), write_tsv(stat_by_taxon)],
-        output_name = "assembly_metadata-~{sample_id}.tsv"
+    if (length(select_all(stat_by_taxon)) > 0) {
+        call utils.concatenate as assembly_stats_non_empty {
+            input:
+                infiles     = [write_tsv([assembly_header]), write_tsv(select_all(stat_by_taxon))],
+                output_name = "assembly_metadata-~{sample_id}.tsv"
+        }
+    }
+    if (length(select_all(stat_by_taxon)) == 0) {
+        call utils.concatenate as assembly_stats_empty {
+            input:
+                infiles     = [write_tsv([assembly_header])],
+                output_name = "assembly_metadata-~{sample_id}.tsv"
+        }
     }
 
     output {
         Array[Map[String,String]] assembly_stats_by_taxon  = stats_by_taxon
-        File   assembly_stats_by_taxon_tsv                 = concatenate.combined
+        File   assembly_stats_by_taxon_tsv                 = select_first([assembly_stats_non_empty.combined, assembly_stats_empty.combined])
         String assembly_method                             = "viral-ngs/scaffold_and_refine_multitaxa"
 
         #String assembly_top_taxon_id               = select_references.top_matches_per_cluster_basenames[0]
diff --git a/test/input/WDL/miniwdl-local/test_inputs-genbank-local.json b/test/input/WDL/miniwdl-local/test_inputs-genbank-local.json
deleted file mode 100644
index 1c938870e..000000000
--- a/test/input/WDL/miniwdl-local/test_inputs-genbank-local.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
-  "genbank.molType": "cRNA",
-  "genbank.reference_accessions": ["KM821997.1", "KM821998.1"],
-  "genbank.coverage_table": "test/input/genbank/coverage_report-RUN1-workflow.txt",
-  "genbank.alignments_bams": [],
-  "genbank.sequencingTech": "Illumina MiSeq",
-  "genbank.biosample_attributes": "test/input/genbank/biosample-attributes-lasv.txt",
-  "genbank.prep_genbank.assembly_method": "placeholder assembly software",
-  "genbank.prep_genbank.assembly_method_version": "5.4.3.2.1",
-  "genbank.comment": "this is only a test -- DO NOT SUBMIT to NCBI",
-  "genbank.author_list": "Odia,Ikponmwosa, Ehaine,Philomena, Oguzie,Judith,U. Siddle,Katherine,J. Mehta,Samar, Barnes,Kayla,M. Winnicki,Sarah,M. Brehio,Patrick, Shah,Rickey,R. Chak,Bridget, Yozwiak,Nathan, Amao,Adebayo, Nosamiefan,Iguosadolo, Birren,Bruce,W. Park,Daniel,J. Folarin,Onikepe, Okokhere,Peter, Sabeti,Pardis,C. Happi,Christian,T.",
-  "genbank.author_sbt_defaults_yaml": "test/input/genbank/default_sbt_values.yaml",
-  "genbank.author_sbt_j2_template": "test/input/genbank/author_template.sbt.j2",
-  "genbank.assemblies_fasta": [
-    "test/input/LASV_NGA_2018_0026.fasta",
-    "test/input/LASV_NGA_2018_0097.fasta",
-    "test/input/LASV_NGA_2018_0541.fasta"
-  ],
-  "genbank.email_address": "viral-ngs@broadinstitute.org"
-}
-