diff --git a/bio/samtools/faidx/test/Snakefile b/bio/samtools/faidx/test/Snakefile
index d15d6fba505..cf366a4235c 100644
--- a/bio/samtools/faidx/test/Snakefile
+++ b/bio/samtools/faidx/test/Snakefile
@@ -38,16 +38,31 @@ rule samtools_faidx_bgzip:
         "master/bio/samtools/faidx"
 
 
-rule samtools_faidx_region:
+rule samtools_faidx_region_file:
     input:
         "{sample}.fa",
         fai="idx/{sample}.fa.fai",
+        regions="{sample}.regions",
     output:
-        "out/{sample}.fas",
+        "out/{sample}.region_file.fas",
     log:
-        "{sample}.region.log",
+        "{sample}.region_file.log",
     params:
-        region="ref",
+        extra="--length 5",
+    wrapper:
+        "master/bio/samtools/faidx"
+
+
+rule samtools_faidx_region_array:
+    input:
+        "{sample}.fa",
+        fai="idx/{sample}.fa.fai",
+    output:
+        "out/{sample}.region_array.fas",
+    log:
+        "{sample}.region_array.log",
+    params:
+        region=["ref", "ref2"],
         extra="--length 5",
     wrapper:
         "master/bio/samtools/faidx"
@@ -59,9 +74,9 @@ rule samtools_faidx_bgzip_region:
         fai="idx/{sample}.fa.bgz.fai",
         gzi="idx/{sample}.fa.bgz.gzi",
     output:
-        "out/{sample}.bgz.fas",
+        "out/{sample}.region_bgzip.fas",
     log:
-        "{sample}.bgzip_region.log",
+        "{sample}.region_bgzip.log",
     params:
         region="ref",
         extra="--length 5",
diff --git a/bio/samtools/faidx/test/genome.regions b/bio/samtools/faidx/test/genome.regions
new file mode 100644
index 00000000000..6415016b862
--- /dev/null
+++ b/bio/samtools/faidx/test/genome.regions
@@ -0,0 +1 @@
+ref
diff --git a/bio/samtools/faidx/wrapper.py b/bio/samtools/faidx/wrapper.py
index 63e44abfa91..3a85b1e177c 100644
--- a/bio/samtools/faidx/wrapper.py
+++ b/bio/samtools/faidx/wrapper.py
@@ -17,10 +17,11 @@
 # Get regions (if present)
 regions = snakemake.input.get("regions", "")
 if regions:
-    regions = f"--regions-file {regions}"
+    regions = f"--region-file {regions}"
 
 region = snakemake.params.get("region", "")
 
+
 # Get FAI and GZI files
 if region or regions:
     fai = snakemake.input.get("fai", "")
diff --git a/test.py b/test.py
index 8ab245518f1..605462538c0 100644
--- a/test.py
+++ b/test.py
@@ -4242,8 +4242,9 @@ def test_samtools_faidx():
             "out/genome.named.fa.fai",
             "out/genome.fas.bgz.fai",
             "out/genome.fas.bgz.gzi",
-            "out/genome.fas",
-            "out/genome.bgz.fas",
+            "out/genome.region_file.fas",
+            "out/genome.region_array.fas",
+            "out/genome.region_bgzip.fas",
             "--use-conda",
             "-F",
         ],