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config_job.file
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config_job.file
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## - - - - - - - - - - - C O N F I G U R A T I O N - F I L E - - - - - - - - - - - - -
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######============== TOOL LOCATIONS ==============######
TOPHAT = /path/to/tophat2
BOWTIE = /path/to/bowtie2
STAR = /path/to/star
HISAT = /path/to/hisat2
BWA = /path/to/bwa/
PICARD = /path/to/picard.jar
GATK = /path/to/gatk.jar
SAMTOOLS = /path/to/samtools #optional
FASTQC = /path/to/fastqc
######============ INPUT FILE OPTIONS ============######
GFF = /path/to/gff_file
GTF = /path/to/gtf_file
GENOME = /path/to/genome_fasta
GENOMEDIR = /path/to/genome_indexes_directory
FASTQ = /path/to/fastq_files/*gz [or false]
SAM = /path/to/sam_files/*sam [or false]
BAM = /path/to/bam_files/*bam [or false]
######================== OPTIONS ==================######
THREADS = 4 #number of threads for alignment process
######=============== OUTPUT FOLDER ===============######
OUTPUTDIR = /path/to/output_folder
######================== WORKFLOW =================######
sampleRNA = true [or false] #is sample RNA
sampleDNA = false [or true] #is sample DNA
#Alignment options
runTopHat = true [or false] #only when sampleRNA=true
runHISAT = true [or false] #only when sampleRNA=true
runSTAR = true [or false] #only when sampleRNA=true
runBWA = false [or true] #only when sampleDNA=true
runBOWTIE = false [or true] #only when sampleDNA=true
#Housekeeping + VariantAnalysis
runFastqc = true [or false]
runVAP = true [or false]
runMergeFilter = true [or false]
######=============== NOTIFICATION ===============######
EMAIL= youremail@address.com
SUBJECT = Title_of_Email #space sensitive
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