diff --git a/pipes/WDL/tasks/tasks_assembly.wdl b/pipes/WDL/tasks/tasks_assembly.wdl
index 522011e01..ad57684be 100644
--- a/pipes/WDL/tasks/tasks_assembly.wdl
+++ b/pipes/WDL/tasks/tasks_assembly.wdl
@@ -652,6 +652,7 @@ task align_reads {
     File   aligned_only_reads_bam_idx    = "~{sample_name}.mapped.bai"
     File   aligned_only_reads_fastqc     = "~{sample_name}.mapped_fastqc.html"
     File   aligned_only_reads_fastqc_zip = "~{sample_name}.mapped_fastqc.zip"
+    Int    reference_length              = read_int("assembly_length")
     Int    reads_provided                = read_int("reads_provided")
     Int    reads_aligned                 = read_int("reads_aligned")
     Int    read_pairs_aligned            = read_int("read_pairs_aligned")
diff --git a/pipes/WDL/workflows/assemble_refbased.wdl b/pipes/WDL/workflows/assemble_refbased.wdl
index 4c72fe4f5..a81ddbba1 100644
--- a/pipes/WDL/workflows/assemble_refbased.wdl
+++ b/pipes/WDL/workflows/assemble_refbased.wdl
@@ -194,7 +194,7 @@ workflow assemble_refbased {
         File        align_to_ref_variants_vcf_gz                 = call_consensus.sites_vcf_gz
         Int         assembly_length                              = call_consensus.assembly_length
         Int         assembly_length_unambiguous                  = call_consensus.assembly_length_unambiguous
-        Int         reference_genome_length                      = plot_ref_coverage.assembly_length
+        Int         reference_genome_length                      = align_to_ref.reference_length[0]
         Float       assembly_mean_coverage                       = plot_ref_coverage.mean_coverage
         
         Int         dist_to_ref_snps                             = call_consensus.dist_to_ref_snps