diff --git a/src/snpeff/config.vsh.yaml b/src/snpeff/config.vsh.yaml
index 8e0d015b..13492392 100644
--- a/src/snpeff/config.vsh.yaml
+++ b/src/snpeff/config.vsh.yaml
@@ -14,269 +14,267 @@ license: MIT
 argument_groups:
   - name: Inputs
     arguments:
-      - name: -input
+      - name: --input
         type: file
         description: Input variants file.
         example: test.vcf
-        direction: input
         required: true
-      - name: -genome_version
+      - name: --genome_version
         type: string
         description: Reference genome version.
         example: GRCh37.75
-        direction: input
         required: true
   - name: Outputs
     arguments:
-      - name: -output
+      - name: --output
         type: file
         description: The output file.
         example: out.vcf
         direction: output
         required: true
-      - name: -summary
+      - name: --summary
         type: file
         description: Summary file directory.
         example: summary_dir
         direction: output
-        required: false
-      - name: -genes
+      - name: --genes
         type: file
         description: Txt file directory.
         example: genes_dir
         direction: output
-        required: false
   - name: Options
     arguments:
-      - name: -chr
+      - name: --chr
         type: string
         description: |
           Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-      - name: -classic
+      - name: --classic
         type: boolean_true
         description: Use old style annotations instead of Sequence Ontology and Hgvs.
-      - name: -csv_stats
+      - name: --csv_stats
         type: file
         description: Create CSV summary file.
-      - name: -download
+      - name: --download
         type: boolean_true
         description: Download reference genome if not available.
-      - name: -input_format
+      - name: --input_format
         alternatives: [-i]
         type: string
         description: |
           Input format [ vcf, bed ]. Default: VCF.
-      - name: -file_list
+          example: "VCF"
+      - name: --file_list
         type: boolean_true
         description: Input actually contains a list of files to process.
-      - name: -output_format
+      - name: --output_format
         alternatives: [-o]
         type: string
         description: |
           Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-      - name: -stats
-        alternatives: [-s, -htmlStats]
+        example: "VCF"
+      - name: --stats
+        alternatives: [-s, --htmlStats]
         type: boolean_true
         description: Create HTML summary file.
-      - name: -no_stats
+      - name: --no_stats
         type: boolean_false
         description: Do not create stats (summary) file.
   - name: Results filter options
     arguments:
-      - name: -fi
-        alternatives: [-filterInterval]
+      - name: --fi
+        alternatives: [--filterInterval]
         type: file
         description: |
           Only analyze changes that intersect with the intervals 
           specified in this file. This option can be used several times.
-      - name: -no_downstream 
+      - name: --no_downstream 
         type: boolean_false
         description: Do not show DOWNSTREAM changes
-      - name: -no_intergenic
+      - name: --no_intergenic
         type: boolean_false
         description: Do not show INTERGENIC changes.
-      - name: -no_intron
+      - name: --no_intron
         type: boolean_false
         description: Do not show INTRON changes.
-      - name: -no_upstream
+      - name: --no_upstream
         type: boolean_false
         description: Do not show UPSTREAM changes.
-      - name: -no_utr
+      - name: --no_utr
         type: boolean_false
         description: Do not show 5_PRIME_UTR or 3_PRIME_UTR changes.
-      - name: -no
+      - name: --no
         type: string
         description: |
           Do not show 'EffectType'. This option can be used several times.
   - name: Annotations options
     arguments:
-      - name: -cancer 
+      - name: --cancer 
         type: boolean_true
         description: Perform 'cancer' comparisons (Somatic vs Germline).
-      - name: -cancer_samples
+      - name: --cancer_samples
         type: file
         description: Two column TXT file defining 'original \t derived' samples.
-      - name: -fastaprot
+      - name: --fastaprot
         type: file
         description: |
           Create an output file containing the resulting protein sequences.
-      - name: -format_eff
+      - name: --format_eff
         type: boolean_true
         description: |
           Use 'EFF' field compatible with older versions (instead of 'ANN').
-      - name: -gene_id
+      - name: --gene_id
         type: boolean_true
         description: Use gene ID instead of gene name (VCF output).
-      - name: -hgvs
+      - name: --hgvs
         type: boolean_true
         description: Use HGVS annotations for amino acid sub-field.
-      - name: -hgvs_old
+      - name: --hgvs_old
         type: boolean_true
         description: Use old HGVS notation.
-      - name: -hgvs1_letter_aa 
+      - name: --hgvs1_letter_aa 
         type: boolean_true
         description: Use one letter Amino acid codes in HGVS notation.
-      - name: -hgvs_tr_id
+      - name: --hgvs_tr_id
         type: boolean_true
         description: Use transcript ID in HGVS notation.
-      - name: -lof
+      - name: --lof
         type: boolean_true
         description: |
           Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
       - name: -no_hgvs
         type: boolean_false
         description: Do not add HGVS annotations.
-      - name: -no_lof
+      - name: --no_lof
         type: boolean_false
         description: Do not add LOF and NMD annotations.
-      - name: -no_shift_hgvs
+      - name: --no_shift_hgvs
         type: boolean_false
         description: |
           Do not shift variants according to HGVS notation (most 3prime end).
-      - name: -oicr
+      - name: --oicr
         type: boolean_true
         description: Add OICR tag in VCF file.
-      - name: -sequence_ontology
+      - name: --sequence_ontology
         type: boolean_true
         description: Use Sequence Ontology terms.
   - name: Generic options
     arguments:
-      - name: -config
+      - name: --config
         alternatives: [-c]
         type: file
         description: Specify config file
-      - name: -config_option
+      - name: --config_option
         type: string
         description: Override a config file option (name=value).
-      - name: -debug
+      - name: --debug
         alternatives: [-d]
         type: boolean_true
         description: Debug mode (very verbose).
-      - name: -data_dir
+      - name: --data_dir
         type: file
         description: Override data_dir parameter from config file.
       # - name: -download
       #   type: boolean_true
       #   description: Download a SnpEff database, if not available locally.
-      - name: -no_download
+      - name: --no_download
         type: boolean_false
         description: Do not download a SnpEff database, if not available locally.
-      - name: -no_log
+      - name: --no_log
         type: boolean_false
         description: Do not report usage statistics to server.
-      - name: -quiet
+      - name: --quiet
         alternatives: [-q]
         type: boolean_true
         description: Quiet mode (do not show any messages or errors)
-      - name: -verbose
+      - name: --verbose
         alternatives: [-v]
         type: boolean_true
         description: Verbose mode.
   - name: Database options
     arguments:
-      - name: -canon 
+      - name: --canon 
         type: boolean_true
         description: Only use canonical transcripts.
-      - name: -canon_list
+      - name: --canon_list
         type: file
         description: |
           Only use canonical transcripts, replace some transcripts using the 'gene_id         
           transcript_id' entries in <file>.
-      - name: -tag
+      - name: --tag
         type: string
         description: |
           Only use transcript having a tag 'tagName'. This option can be used multiple times.
-      - name: -no_tag
+      - name: --no_tag
         type: boolean_false
         description: |
           Filter out transcript having a tag 'tagName'. This option can be used multiple times.
-      - name: -interaction
+      - name: --interaction
         type: boolean_true
         description: Annotate using interactions (requires interaction database).
-      - name: -interval
+      - name: --interval
         type: file
         description: |
           Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times).
-      - name: -max_tsl
+      - name: --max_tsl
         type: integer
         description: Only use transcripts having Transcript Support Level lower than <TSL_number>.
-      - name: -motif 
+      - name: --motif 
         type: boolean_true
         description: Annotate using motifs (requires Motif database).
-      - name: -nextprot
+      - name: --nextprot
         type: boolean_true
         description: Annotate using NextProt (requires NextProt database).
-      - name: -no_genome
+      - name: --no_genome
         type: boolean_false
         description: Do not load any genomic database (e.g. annotate using custom files).
-      - name: -no_expand_iub
+      - name: --no_expand_iub
         type: boolean_false
         description: Disable IUB code expansion in input variants.
-      - name: -no_interaction
+      - name: --no_interaction
         type: boolean_false
         description: Disable inteaction annotations.
-      - name: -no_motif
+      - name: --no_motif
         type: boolean_false
         description: Disable motif annotations.
-      - name: -no_nextprot
+      - name: --no_nextprot
         type: boolean_false
         description: Disable NextProt annotations.
-      - name: -only_reg
+      - name: --only_reg
         type: boolean_true
         description: Only use regulation tracks.
-      - name: -only_protein
+      - name: --only_protein
         type: boolean_true
         description: Only use protein coding transcripts.
-      - name: -only_tr
+      - name: --only_tr
         type: file
         description: |
           Only use the transcripts in this file. Format: One transcript ID per line.
         example: file.txt
-      - name: -reg
+      - name: --reg
         type: string
         description: Regulation track to use (this option can be used add several times).
-      - name: -ss
-        alternatives: [-spliceSiteSize]
+      - name: --ss
+        alternatives: [--spliceSiteSize]
         type: integer
         description: |
           Set size for splice sites (donor and acceptor) in bases. Default: 2.
-      - name: -splice_region_exon_size
+      - name: --splice_region_exon_size
         type: integer
         description: |
           Set size for splice site region within exons. Default: 3 bases.
-      - name: -splice_region_intron_min
+      - name: --splice_region_intron_min
         type: integer
         description: |
           Set minimum number of bases for splice site region within intron. Default: 3 bases.
-      - name: -splice_region_intron_max
+      - name: --splice_region_intron_max
         type: integer
         description: |
           Set maximum number of bases for splice site region within intron. Default: 8 bases.
-      - name: -strict
+      - name: --strict
         type: boolean_true
         description: Only use 'validated' transcripts (i.e. sequence has been checked).
-      - name: -ud
-        alternatives: [-upDownStreamLen]
+      - name: --ud
+        alternatives: [--upDownStreamLen]
         type: integer
         description: Set upstream downstream interval length (in bases).
 resources:
@@ -293,10 +291,9 @@ engines:
     setup:
       - type: docker
         run: |
-          # touch ./var/software_versions.txt && \
-          # version=$(snpEff -version) && \
-          # version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \
-          # echo "$version_trimmed" > ./var/software_versions.txt
+          version=$(snpEff -version) && \
+          version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \
+          echo "$version_trimmed" > /var/software_versions.txt
 runners:
   - type: executable
   - type: nextflow
\ No newline at end of file
diff --git a/src/snpeff/script.sh b/src/snpeff/script.sh
index a3770e34..975c8eb9 100644
--- a/src/snpeff/script.sh
+++ b/src/snpeff/script.sh
@@ -150,4 +150,6 @@ if [ -z "$par_no_stats" ]; then
     else
     mv -f snpEff_genes.txt "$directory_path"
     fi
-fi
\ No newline at end of file
+fi
+
+exit 0
\ No newline at end of file
diff --git a/src/snpeff/test.sh b/src/snpeff/test.sh
index 2185c70a..241deb67 100644
--- a/src/snpeff/test.sh
+++ b/src/snpeff/test.sh
@@ -3,8 +3,6 @@
 set -eo pipefail
 
 ## VIASH START
-meta_executable="$PWD/target/executable/snpeff/snpeff"
-meta_resources_dir="$PWD/src/snpeff"
 ## VIASH END
 
 ###########################################################################
@@ -16,9 +14,9 @@ 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
+  --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")
@@ -50,11 +48,11 @@ pushd test2 > /dev/null
 
 echo "> Run Test 2: different input + options"
 "$meta_executable" \
-  -genome_version GRCh37.75 \
-  -input "$meta_resources_dir/test_data/test.vcf" \
-  -interval "$meta_resources_dir/test_data/my_annotations.bed" \
-  -no_stats \
-  -output output.vcf
+  --genome_version GRCh37.75 \
+  --input "$meta_resources_dir/test_data/test.vcf" \
+  --interval "$meta_resources_dir/test_data/my_annotations.bed" \
+  --no_stats \
+  --output output.vcf
 
 # Check if output.vcf exists
 if [ ! -e "output.vcf" ]; then
@@ -89,11 +87,11 @@ mkdir temp
 
 echo "> Run Test 3: move output files"
 "$meta_executable" \
-  -genome_version GRCh37.75 \
-  -input "$meta_resources_dir/test_data/test.vcf" \
-  -output output.vcf \
-  -summary temp \
-  -genes temp
+  --genome_version GRCh37.75 \
+  --input "$meta_resources_dir/test_data/test.vcf" \
+  --output output.vcf \
+  --summary temp \
+  --genes temp
 
 # Check if output.vcf exists
 if [ ! -e "output.vcf" ]; then