diff --git a/download_genes.nf b/download_genes.nf
index 3d72ae4..bf8c3d5 100644
--- a/download_genes.nf
+++ b/download_genes.nf
@@ -46,11 +46,13 @@ workflow {
     // Parse the CSV path(s), if provided
     Channel
         .fromPath( params.genome_csv.split(',').toList() )
+        .filter { it.exists() }
         .set { gene_manifest_csv }
 
     // Parse the TSV path(s), if provided
     Channel
         .fromPath( params.genome_tsv.split(',').toList() )
+        .filter { it.exists() }
         .set { gene_manifest_tsv }
 
     // Download the genes for each genome
diff --git a/download_genomes.nf b/download_genomes.nf
index f90349c..92b0795 100644
--- a/download_genomes.nf
+++ b/download_genomes.nf
@@ -46,11 +46,13 @@ workflow {
     // Parse the CSV path(s), if provided
     Channel
         .fromPath( params.genome_csv.split(',').toList() )
+        .filter { it.exists() }
         .set { genome_manifest_csv }
 
     // Parse the TSV path(s), if provided
     Channel
         .fromPath( params.genome_tsv.split(',').toList() )
+        .filter { it.exists() }
         .set { genome_manifest_tsv }
 
     // Download the genomes for each genome