diff --git a/src/snpeff/script.sh b/src/snpeff/script.sh
index d7c1ae97..9c6d94f5 100644
--- a/src/snpeff/script.sh
+++ b/src/snpeff/script.sh
@@ -74,7 +74,7 @@ snpEff \
     ${par_stats:+-stats} \
     ${par_noStats:+-noStats} \
     ${par_fi:+-fi "$par_fi"} \
-    ${par_no_downstream :+-no-downstream } \
+    ${par_no_downstream:+-no-downstream} \
     ${par_no_intergenic:+-no-intergenic} \
     ${par_no_intron:+-no-intron} \
     ${par_no_upstream:+-no-upstream} \
@@ -103,7 +103,7 @@ snpEff \
     ${par_noLog:+-noLog} \
     ${par_quiet:+-quiet} \
     ${par_verbose:+-verbose} \
-    ${par_canon :+-canon} \
+    ${par_canon:+-canon} \
     ${par_canonList:+-canonList "$par_canonList"} \
     ${par_tag:+-tag "$par_tag"} \
     ${par_notag:+-notag} \
@@ -129,4 +129,14 @@ snpEff \
     ${par_ud:+-ud "$par_ud"} \
     "$par_genome_version" \
     "$par_input" \
-    > "$par_output"
\ No newline at end of file
+    > "$par_output"
+
+# Path of the output file (par_output)
+absolute_path=$(realpath "$par_output")
+directory_path=$(dirname "$absolute_path")
+
+# Move the automatically generated outputs to the pwd
+if [ -z "$par_noStats" ]; then
+    mv -f snpEff_genes.txt snpEff_summary.html "$directory_path"
+fi
+# mv -f snpEff_genes.txt "$directory_path"
\ No newline at end of file
diff --git a/src/snpeff/test.sh b/src/snpeff/test.sh
new file mode 100644
index 00000000..9f3fc057
--- /dev/null
+++ b/src/snpeff/test.sh
@@ -0,0 +1,83 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+meta_executable="$PWD/target/executable/snpeff/snpeff"
+meta_resources_dir="$PWD/src/snpeff"
+## VIASH END
+
+###########################################################################
+
+# Test 1: Run SnpEff with only required parameters
+
+mkdir test1
+pushd test1 > /dev/null # cd test1 (stack)
+
+echo "> Run Test 1: required parameters"
+"$meta_executable" \
+  -genome_version GRCh37.75 \
+  -input "$meta_resources_dir/test_data/cancer.vcf" \
+  -output out.vcf
+
+# Check if output files are generated
+output_files=("out.vcf" "snpEff_genes.txt" "snpEff_summary.html")
+
+# Check if any of the files do not exist
+for file in "${output_files[@]}"; do
+    if [ ! -e "$file" ]; then
+        echo "File $file does not exist."
+    fi
+done
+
+# Check if files are empty
+for file in "${output_files[@]}"; do
+    if [ ! -s "$file" ]; then
+        echo "File $file is empty."
+    fi
+done
+
+popd > /dev/null # Remove directory from stack (LIFO)
+
+echo "Test 1 succeeded."
+
+###########################################################################
+
+# Test 2: Run SnpEff with a different input + options
+
+# mkdir test2
+# pushd test2 > /dev/null
+
+# echo "> Run Test 2: different input + options"
+# "$meta_executable" \
+#   -genome_version GRCh37.66 \
+#   -input "$meta_resources_dir/test_data/test.vcf" \
+#   -interval "$meta_resources_dir/test_data/my_annotations.bed" \
+#   -noStats \
+#   -output output.vcf
+
+# # Check if out.vcf exists
+# if [ ! -e "output.vcf" ]; then
+#     echo "File out.vcf does not exist."
+# fi
+
+# # These files should not exist
+# files=("snpEff_genes.txt" "snpEff_summary.html")
+# for file in "${files[@]}"; do
+#     if [ -e "$file" ]; then
+#         echo "Error: File $file exists."
+#     fi
+# done
+
+# # Check if output.vcf is empty
+# if [ ! -s "output.vcf" ]; then
+#     echo "File output.vcf is empty."
+# fi
+
+# popd > /dev/null
+
+# echo "Test 2 succeeded."
+
+###########################################################################
+
+echo "All tests successfully completed!"
\ No newline at end of file
diff --git a/src/snpeff/test_data/cancer.vcf b/src/snpeff/test_data/cancer.vcf
new file mode 100644
index 00000000..f37ad8c3
--- /dev/null
+++ b/src/snpeff/test_data/cancer.vcf
@@ -0,0 +1,2 @@
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient_01_Germline	Patient_01_Somatic
+1	69091	.	A	C,G	.	PASS	AC=1	GT	1/0	2/1
diff --git a/src/snpeff/test_data/my_annotations.bed b/src/snpeff/test_data/my_annotations.bed
new file mode 100644
index 00000000..a5247f97
--- /dev/null
+++ b/src/snpeff/test_data/my_annotations.bed
@@ -0,0 +1 @@
+1	10000	20000	MY_ANNOTATION
diff --git a/src/snpeff/test_data/script.sh b/src/snpeff/test_data/script.sh
index 7ad31ac3..a47ec136 100644
--- a/src/snpeff/test_data/script.sh
+++ b/src/snpeff/test_data/script.sh
@@ -1,7 +1,15 @@
-# clone repo
-if [ ! -d /tmp/snakemake-wrappers ]; then
-  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+# Test files from SnpEff examples
+if [ ! -f snpEff_latest_core.zip ]; then
+    wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip
 fi
 
-# copy test data
-cp -r /tmp/snakemake-wrappers/bio/snpeff/annotate/test/*.vcf src/snpeff/test_data/test.vcf
\ No newline at end of file
+if [ ! -d snpEff ]; then
+    unzip snpEff_latest_core.zip
+fi
+
+mv snpEff/examples/test.vcf src/snpeff/test_data/
+mv snpEff/examples/cancer.vcf src/snpeff/test_data/
+mv snpEff/examples/my_annotations.bed src/snpeff/test_data/
+
+rm -rf snpEff_latest_core.zip
+rm -rf snpEff
\ No newline at end of file
diff --git a/src/snpeff/test_data/test.vcf b/src/snpeff/test_data/test.vcf
index 64c949d0..d552ef18 100644
--- a/src/snpeff/test_data/test.vcf
+++ b/src/snpeff/test_data/test.vcf
@@ -1,8 +1 @@
-##fileformat=VCFv4.1
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##contig=<ID="KJ660346.1",length=18957>
-##reference=http://www.ncbi.nlm.nih.gov/nuccore/KJ660346.1
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	fake_KJ660346
-KJ660346	3116	.	C	T	.	.	.	GT	1
-KJ660346	10743	.	T	G	.	.	.	GT	1
-KJ660346	15660	.	C	A	.	.	.	GT	1
+1	10469	.	C	G	365.78	PASS	AC=30;AF=0.0732