diff --git a/workflows/euryale.nf b/workflows/euryale.nf
index 7f899ab..7b9f06c 100644
--- a/workflows/euryale.nf
+++ b/workflows/euryale.nf
@@ -72,7 +72,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
 def multiqc_report = []
 
 workflow EURYALE {
-    if (params.reference_fasta == null && params.diamond_db == null) { exit 1, 'A reference fasta (--reference_fasta) or a DIAMOND db (--diamond_db) must be specified' }
+    if (params.reference_fasta == null && params.diamond_db == null && params.skip_alignment == false) { exit 1, 'A reference fasta (--reference_fasta) or a DIAMOND db (--diamond_db) must be specified' }
     if (params.run_kaiju == true && params.kaiju_db == null) {exit 1, 'A Kaiju tar.gz database must be specified with --kaiju_db'}
     if (params.run_kraken2 == true && params.kraken2_db == null) {exit 1, 'A Kraken2 database must be specified with --kraken2_db'}
     if (params.host_fasta == null && params.bowtie2_db == null && params.skip_host_removal == false) {exit 1, 'Either a host reference FASTA (--host_fasta) or a pre-built bowtie2 index (--bowtie2_db) must be specified'}