diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3c5cf149..afc10d1f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -135,6 +135,12 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to arriba output"
                 },
+                "ctatsplicing_ref": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Path to ctatsplicing references"
+                },
                 "download_refs": {
                     "type": "boolean",
                     "fa_icon": "far fa-file-code",
diff --git a/subworkflows/local/build_references/main.nf b/subworkflows/local/build_references/main.nf
index a7e9e859..77422d78 100644
--- a/subworkflows/local/build_references/main.nf
+++ b/subworkflows/local/build_references/main.nf
@@ -146,7 +146,10 @@ workflow BUILD_REFERENCES {
 
     def ch_starfusion_ref = Channel.empty()
     if (tools.intersect(["starfusion", "ctatsplicing", "fusioninspector"])) {
-        if (!exists_not_empty(params.starfusion_ref)) {
+        if (exists_not_empty(params.starfusion_ref)) {
+            ch_starfusion_ref = Channel.fromPath(params.starfusion_ref).map { it -> [[id:it.name], it] }
+        }
+        else {
             if(!params.fusion_annot_lib) {
                 error("Expected --fusion_annot_lib to be specified when using StarFusion or any tools that depend on it")
             }
@@ -178,19 +181,14 @@ workflow BUILD_REFERENCES {
 
             STARFUSION_BUILD(ch_fasta, ch_gtf, params.fusion_annot_lib, params.species, pfam_file, dfam_urls_ch, params.annot_filter_url)
             ch_versions = ch_versions.mix(STARFUSION_BUILD.out.versions)
-            if (tools.contains("ctatsplicing")) {
-                CTATSPLICING_PREPGENOMELIB(
-                    STARFUSION_BUILD.out.reference,
-                    params.ctatsplicing_cancer_introns
-                )
-                ch_versions = ch_versions.mix(CTATSPLICING_PREPGENOMELIB.out.versions)
-                ch_starfusion_ref = CTATSPLICING_PREPGENOMELIB.out.reference
-            } else {
-                ch_starfusion_ref = STARFUSION_BUILD.out.reference
-            }
         }
-        else {
-            ch_starfusion_ref = Channel.fromPath(params.starfusion_ref).map { it -> [[id:it.name], it] }
+        if (tools.contains("ctatsplicing") && !exists_not_empty(params.ctatsplicing_ref)) {
+            CTATSPLICING_PREPGENOMELIB(
+                ch_starfusion_ref,
+                params.ctatsplicing_cancer_introns
+            )
+            ch_versions = ch_versions.mix(CTATSPLICING_PREPGENOMELIB.out.versions)
+            ch_starfusion_ref = CTATSPLICING_PREPGENOMELIB.out.reference
         }
     }