diff --git a/modules.json b/modules.json
index 5b778895..a061424c 100644
--- a/modules.json
+++ b/modules.json
@@ -267,7 +267,7 @@
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "bf8ff98531167f8245ba5c44ce7d781503ddf936",
+                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
index c1e8ef3a..59ed3088 100644
--- a/modules/nf-core/samtools/faidx/main.nf
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -35,8 +35,12 @@ process SAMTOOLS_FAIDX {
     """
 
     stub:
+    def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll()
+    def fastacmd = match[0] ? "touch ${match[0][1]}" : ''
     """
+    ${fastacmd}
     touch ${fasta}.fai
+
     cat <<-END_VERSIONS > versions.yml
 
     "${task.process}":