config_job.file

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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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