diff --git a/pipes/WDL/workflows/augur_from_assemblies.wdl b/pipes/WDL/workflows/augur_from_assemblies.wdl
index e94ee5574..08c3ab87e 100644
--- a/pipes/WDL/workflows/augur_from_assemblies.wdl
+++ b/pipes/WDL/workflows/augur_from_assemblies.wdl
@@ -13,6 +13,7 @@ workflow augur_from_assemblies {
 
     input {
         Array[File]+   assembly_fastas
+        Array[File]?   contextual_genome_fastas
         Array[File]+   sample_metadata_tsvs
         File           ref_fasta
 
@@ -29,6 +30,10 @@ workflow augur_from_assemblies {
           description: "Set of assembled genomes to align and build trees. These must represent a single chromosome/segment of a genome only. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture.",
           patterns: ["*.fasta", "*.fa", "*.fasta.gz", "*.fasta.zst"]
         }
+        contextual_genome_fastas: {
+          description: "Set of near-complete contextual genomes to include in tree build. Each fasta provided must represent a single chromosome/segment of a genome. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture. ",
+          patterns: ["*.fasta", "*.fa", "*.fasta.gz", "*.fasta.zst"]
+        }
         sample_metadata_tsvs: {
             description: "Tab-separated metadata file that contain binning variables and values. Must contain all samples: output will be filtered to the IDs present in this file.",
             patterns: ["*.txt", "*.tsv"]
@@ -54,7 +59,7 @@ workflow augur_from_assemblies {
 
     call utils.zcat {
         input:
-            infiles     = assembly_fastas,
+            infiles     = flatten([assembly_fastas, select_first([contextual_genome_fastas,[]])]),
             output_name = "all_samples_combined_assembly.fasta"
     }
     call utils.filter_sequences_by_length {