Reorder parameters

Author: nicolaasuni

resources/tools/vcfnorm.sh

@@ -32,10 +32,10 @@ cat "${REFERENCE_GENOME_FASTA_FILE}" | sed 's/>chrM/>MT/g' | sed 's/>chr/>/g' >
 vt index "${VCF_INPUT_FILE}"
 
 # Decompose multiallelic variants into biallelic variants
-vt decompose -s "${VCF_INPUT_FILE}" -o decomposed.vcf
+vt decompose -s -o decomposed.vcf "${VCF_INPUT_FILE}"
 
 # Normalize variants (https://academic.oup.com/bioinformatics/article/31/13/2202/196142)
-vt normalize decomposed.vcf -m -r genome.fa -o "${VCF_OUTPUT_NAME}.vcf"
+vt normalize -m -r genome.fa -o "${VCF_OUTPUT_NAME}.vcf" decomposed.vcf
 
 # Remove temporary file
 rm -f decomposed.vcf