diff --git a/modules.json b/modules.json
index 2efbb154..d77a8341 100644
--- a/modules.json
+++ b/modules.json
@@ -20,7 +20,8 @@
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "d593e8f6b7d1bbbb2acf43a4b9efeeac8d6720f2",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/cat/cat/cat-cat.diff"
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
diff --git a/modules/nf-core/cat/cat/cat-cat.diff b/modules/nf-core/cat/cat/cat-cat.diff
new file mode 100644
index 00000000..4d2fedae
--- /dev/null
+++ b/modules/nf-core/cat/cat/cat-cat.diff
@@ -0,0 +1,34 @@
+Changes in module 'nf-core/cat/cat'
+--- modules/nf-core/cat/cat/main.nf
++++ modules/nf-core/cat/cat/main.nf
+@@ -22,6 +22,8 @@
+     def args2 = task.ext.args2 ?: ''
+     def file_list = files_in.collect { it.toString() }
+ 
++    // choose appropriate concatenation tool depending on input and output format
++
+     // | input     | output     | command1 | command2 |
+     // |-----------|------------|----------|----------|
+     // | gzipped   | gzipped    | cat      |          |
+@@ -30,7 +32,7 @@
+     // | ungzipped | gzipped    | cat      | pigz     |
+ 
+     // Use input file ending as default
+-    prefix   = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
++    prefix   = task.ext.prefix ?: "${meta.id}${getFileSuffix(file_list[0])}"
+     out_zip  = prefix.endsWith('.gz')
+     in_zip   = file_list[0].endsWith('.gz')
+     command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
+@@ -68,3 +70,10 @@
+     END_VERSIONS
+     """
+ }
++
++// for .gz files also include the second to last extension if it is present. E.g., .fasta.gz
++def getFileSuffix(filename) {
++    def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/
++    return match ? match[0][1] : filename.substring(filename.lastIndexOf('.'))
++}
++
+
+************************************************************
diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf
index 970ab760..adbdbd7b 100644
--- a/modules/nf-core/cat/cat/main.nf
+++ b/modules/nf-core/cat/cat/main.nf
@@ -22,6 +22,8 @@ process CAT_CAT {
     def args2 = task.ext.args2 ?: ''
     def file_list = files_in.collect { it.toString() }
 
+    // choose appropriate concatenation tool depending on input and output format
+
     // | input     | output     | command1 | command2 |
     // |-----------|------------|----------|----------|
     // | gzipped   | gzipped    | cat      |          |
@@ -30,7 +32,7 @@ process CAT_CAT {
     // | ungzipped | gzipped    | cat      | pigz     |
 
     // Use input file ending as default
-    prefix   = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
+    prefix   = task.ext.prefix ?: "${meta.id}${getFileSuffix(file_list[0])}"
     out_zip  = prefix.endsWith('.gz')
     in_zip   = file_list[0].endsWith('.gz')
     command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
@@ -68,3 +70,10 @@ process CAT_CAT {
     END_VERSIONS
     """
 }
+
+// for .gz files also include the second to last extension if it is present. E.g., .fasta.gz
+def getFileSuffix(filename) {
+    def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/
+    return match ? match[0][1] : filename.substring(filename.lastIndexOf('.'))
+}
+