I am using it by using sbatch, and calling the .py script it contains:

import subprocess
import argparse
import time
import sys

if __name__== "__main__":

parser  = argparse.ArgumentParser(description = "VarDictJava")

    parser.add_argument('-o', '--outDir',
                        dest = "outDir",
                        action = "store",
                        required=True,
                        help = "Path to out Working Directory.")

    parser.add_argument('-cleanBqsrBam', '--cleanBqsrBam',
                                            dest = "cleanBqsrBam",
                                            action = "store",
                                            help = "bam")

    parser.add_argument('-refGenome', '--refGenome',
                                            dest = "refGenome",
                                            action = "store",
                                            help = "refGenome")

    parser.add_argument('-targetBedFile', '--targetBedFile',
                                            dest = "targetBedFile",
                                            action = "store",
                                            help = "samtoolsPath")

    parser.add_argument('-sample', '--sample',
                                            dest = "sample",
                                            action = "store",
                                            help = "sample name")

    parser.add_argument('-cpus', '--cpus',
                                            dest = "cpus",
                                            action = "store",
                                            help = "cpus")
    options = parser.parse_args()

    cleanBqsrBam = options.cleanBqsrBam
    refGenome = options.refGenome
    outDir = options.outDir
    targetBedFile = options.targetBedFile
    sample = options.sample
    cpus = options.cpus
    start_time = time.time()


    LOG_FILE_OUT = open(outDir+"/error_VARDICT/logout_VARDICT_"+sample+".txt", 'w')

    LOG_FILE_ERR = open(outDir+"/error_VARDICT/logerr_VARDICT_"+sample+".txt", 'w')

    bashArguments = "/apps/VARDICTJAVA/1.8.3/bin/VarDict -G "+refGenome+" -f 0.001 -N "+sample+" -b "+cleanBqsrBam+" -c 1 -S 2 -E 3 -g 4 "+targetBedFile+" | teststrandbias.R | var2vcf_valid.pl -N "+sample+" -E -f 0.001  > vars.vcf"

But even so, it does not detect the .R or the .pl I try to call when I use the basharguments. In the /apps/VARDICTJAVA/1.8.3/bin> folder, there is only: VarDict VarDict.bat.