diff --git a/modules.json b/modules.json
index a3017f7..7eb15e3 100644
--- a/modules.json
+++ b/modules.json
@@ -73,7 +73,8 @@
                     "falco": {
                         "branch": "master",
                         "git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/falco/falco.diff"
                     },
                     "fastp": {
                         "branch": "master",
diff --git a/modules/nf-core/falco/falco.diff b/modules/nf-core/falco/falco.diff
new file mode 100644
index 0000000..4c726b9
--- /dev/null
+++ b/modules/nf-core/falco/falco.diff
@@ -0,0 +1,16 @@
+Changes in module 'nf-core/falco'
+--- modules/nf-core/falco/main.nf
++++ modules/nf-core/falco/main.nf
+@@ -33,7 +33,9 @@
+         """
+     } else {
+         """
+-        falco $args --threads $task.cpus ${reads}
++        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
++        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
++        falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
+ 
+         cat <<-END_VERSIONS > versions.yml
+         "${task.process}":
+
+************************************************************