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config_wgs.xml
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<dependencies>
<module>
<bwa>
<value version="0.7.8"></value>
</bwa>
</module>
<module>
<samtools>
<value version="1.3.1"></value>
</samtools>
</module>
<module>
<R>
<value version="3.4.0"></value>
</R>
</module>
<module>
<gatk>
<value version="3.8"></value>
</gatk>
</module>
<tool>
<value name="java"></value>
<value version="jdk1.8.0_112/bin/java"></value>
<value location="/cluster/software/VERSIONS/java/"></value>
</tool>
<tool>
<value name="trimmomatic"></value>
<value version="Trimmomatic-0.33/trimmomatic-0.33.jar"></value>
<value location="/cluster/shared/bioinformatics/src/"></value>
<value required="java"></value>
</tool>
<tool>
<value name="picard"></value>
<value version="picard-tools-1.129/picard.jar"></value>
<value location="/cluster/shared/bioinformatics/src/"></value>
<value required="java"></value>
</tool>
<tool>
<value name="gatk"></value>
<value version="gatk-3.8/GenomeAnalysisTK.jar"></value>
<value location="/cluster/software/VERSIONS/"></value>
<value required="java"></value>
</tool>
<file>
<value name="adapters"></value>
<value location="/cluster/shared/bioinformatics/src/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa"></value>
</file>
<file>
<value name="reference"></value>
<value location="/cluster/shared/bioinformatics/reference-data/b37/GATK2.8/human_g1k_v37_decoy.fasta"></value>
</file>
<file>
<value name="known_snps"></value>
<value location="/cluster/shared/bioinformatics/reference-data/b37/GATK2.8/dbsnp_138.b37.vcf"></value>
</file>
<file>
<value name="known_indels"></value>
<value location="/cluster/shared/bioinformatics/reference-data/b37/GATK2.8/Mills_and_1000G_gold_standard.indels.b37.vcf"></value>
</file>
<file>
<value name="hapmap"></value>
<value location="/cluster/shared/bioinformatics/reference-data/b37/GATK2.8/hapmap_3.3.b37.vcf"></value>
</file>
<file>
<value name="omni"></value>
<value location="/cluster/shared/bioinformatics/reference-data/b37/GATK2.8/1000G_omni2.5.b37.vcf"></value>
</file>
<file>
<value name="snps_1kg"></value>
<value location="/cluster/shared/bioinformatics/reference-data/b37/GATK2.8/1000G_phase1.snps.high_confidence.b37.vcf"></value>
</file>
<file>
<value name="indels_1kg"></value>
<value location="/cluster/shared/bioinformatics/reference-data/b37/GATK2.8/1000G_phase1.indels.b37.vcf"></value>
</file>
</dependencies>