parameterfile_NRef.init

#! /bin/bash

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# TypeTE - parameterfile_NRef.init        #
#                                         #
# configuration file for the pipeline     #
#                                         #
# Author: Clement Goubert                 #
# Date: 03/14/2019                        #
# Version: 1.0                            #
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### MAIN PARAMETERS

# user data
VCF="/workdir/cg629/bin/TypeTE/test_data/test_data_nonref.vcf" #Path to MELT vcf (.vcf or .vcf.gz) must contain INFO field with TSD and MEI type
BAMPATH="/workdir/cg629/Projects/TypeTE_tutorial/test_data/" # Path to the bams folder
BAMFILE="/workdir/cg629/bin/TypeTE/test_data/input_table.txt" # <indiv_name> <bam_name> (2 fields tab separated table)

# genome data
RM_TRACK="/workdir/cg629/bin/TypeTE/Ressources/RepeatMasker_Alu_hg19.bed" # set by default for hg19
RM_FASTA="/workdir/cg629/bin/TypeTE/Ressources/refinelib" # set by default to be compatible with the Repeat Masker track included in the package
GENOME="/workdir/cg629/Projects/testTypeTE/hs37d5.fa" # Path the the reference genome sequence

# output
OUTDIR="/workdir/cg629/Projects/TypeTE_tutorial" # Path to place the output directory (will be named after PROJECT); OUTDIR must exist
PROJECT="OUTPUTS_NRef_testdata" # Name of the project (name of the folder)

# multi-threading
individual_nb="1" # number of individual per job (try to minimize that number)
CPU="3" # number of CPU (try to maximize that number) # CPU x individual_nb >= total # of individuals

## non-mendatory parameters
MAP="NO" #OR NO (experimental)

### DEPENDENCIES PATH
# /!\ PERL MUST BE IN PATH /!\
PARALLEL="/programs/parallel/bin/parallel" #Path to the GNU Parallel program
PICARD="/programs/picard-tools-2.9.0" #Path to Picard Tools
BEDTOOLS="/programs/bedtools-2.27.1/bin/bedtools" #Path to bedtools executable
SEQTK="/programs/seqtk" #Path to seqtk executable
BAMUTILS="/programs/bamUtil" #Path to bamUtil
SPADES="/programs/spades-3.5.0/bin" #Path to spades bin directory (to locate spades.py and dispades.py)
MINIA="/workdir/cg629/bin/minia/build/bin" #Path to minia bin directory
CAP3="/workdir/cg629/bin/CAP3" #Path to CAP3 directory
BLAST="/programs/ncbi-blast-2.7.1+/bin" #Path to blast bin directory
BWA="/programs/bwa-0.5.9/bwa" #Path to bwa executable
BGZIP="bgzip" #Path to bgzip executable
TABIX="tabix" #Path to tabix executable