#### path to all the tools and references to run workflow

#### references
#BLAT_REF=@REFERENCE@/hg19/hg19.2bit
CHROMSIZE=@REFERENCE@/hg19/chromsize.txt
#dbSNP_REF=@REFERENCE@/hg19/dbsnp_135.hg19.vcf.gz
FEATURES=@REFERENCE@/hg19/genes_Illumina_iGenomes.gtf
HAPMAP_VCF=@REFERENCE@/hg19/hapmap_3.3.hg19.sites.vcf
OMNI_VCF=@REFERENCE@/hg19/1000G_omni2.5.hg19.sites.vcf
MASTER_GENE_FILE=@REFERENCE@/hg19/hg19.master.gene.bed
REF_BOWTIE=@REFERENCE@/hg19/37.1/indexed/allchr
REF_FLAT=@REFERENCE@/hg19/hg19.refflat
REF_GENOME=@REFERENCE@/hg19/37.1/allchr.fa
REF_GENE_BED=@REFERENCE@/hg19/hg19_refGene_table.bed
REF_SAMPLE_BED=@REFERENCE@/hg19/hg19_sample_table.bed
TRANSCRIPTOME_HG19_INDEX=@REFERENCE@/transcriptome/hg19/index


#### references required for tophat-fusion-post
ENSGENE=@REFERENCE@/hg19/ensGene.txt
#HG_BLAST_DB=@REFERENCE@/blast_db/human_genomic
KARYOTYPE=@REFERENCE@/hg19/karyotype.human.hg19.txt
MCL=@REFERENCE@/hg19/mcl
#NT_BLAST_DB=@REFERENCE@/blast_db/nt
REFGENE=@REFERENCE@/hg19/refGene.txt


#### tools
BEDTOOLS=@BINARY@/bedtools/2.17.0
BLAT=@BINARY@/blat/34
BLASTC=@BINARY@/blast/2.2.28/bin
BOWTIE=@BINARY@/bowtie/2.1.0
BOWTIE1=@BINARY@/bowtie/0.12.9
CIRCOS=@BINARY@/circos/0.64/bin
FASTQC=@BINARY@/fastqc/0.10.1
GATK=@BINARY@/gatk/1.6
HTSEQ=@BINARY@/htseq/0.5.3p9
JAVA=@JAVA@
TOPHAT=@BINARY@/tophat/2.0.6
PERL=@PERL@
PICARD=@BINARY@/picard/1.92
PYTHON=@PYTHON@
R=@R@
RSEQC=@BINARY@/rseqc/2.3.7/bin
SAMTOOLS=@BINARY@/samtools/0.1.19
SUBREAD_BIN=@BINARY@/subread/1.4.4
WORKFLOW_PATH=@SOURCE@
UCSC_BIN=@BINARY@/ucsc


#### env variables
HTSEQPATH=@BINARY@/htseq/0.5.3p9/lib/python2.7/site-packages
PYTHONPATH=@PYTHONPATH@
RSEQCPATH=@BINARY@/rseqc/2.3.7/lib/python2.7/site-packages
STD_PERL5LIB=/usr/lib/perl5:/usr/lib64/perl5:@LIBRARY@/perl5/lib/perl5:@LIBRARY@/perl5/lib/perl5/x86_64-linux:@LIBRARY@/perl5/lib/perl5/x86_64-linux/auto

#### value for dashboard update can be yes/no
DASHBOARD_UPDATE=NO
STANDALONE=YES


#### queue
QUEUE=ngs-test
GATK_QUEUE=ngs-sec -l medp~TRUE


#### Queue parameters
NOTIFICATION_OPTION=a


#### Program parameters

#### leave fusion blank for human run or set it "-non-human" (without quotes) for others.
FUSION=
SEGMENT_SIZE=25

MAX_HITS=20
INSERT_SIZE=50
MATE_SD=20
FUSION_MIN_DIST=50000

GATK_UG_PARAM=
GATK_VQSR_FEATURES=ReadPosRankSum:FS
GATK_VQSR_GAUSSIANS=4
GATK_VQSR_PCT_BAD_VARIANTS=0.05
GATK_VQSR_TRENCH=99.0 
GATK_HARD_FILTERS_EXP="FS > 20.0":"ED > 5":"ReadPosRankSum < -8.0":"ReadPosRankSum >-8.0"
GATK_HARD_FILTERS_NAMES=FSFilter:EDFilter:RPRSFilter:RPRSFilter

