trio_whole_exome_config.sh

#!/usr/bin/bash
#
# Basic configuration options for trio WES pipeline
#

SCRIPTS=/home/u035/project/scripts
BCBIO_TEMPLATE=$SCRIPTS/trio_whole_exome_bcbio_template.yaml
TARGET=/home/u035/project/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
DOWNLOAD_DIR=/scratch/u035/project/trio_whole_exome/data
REFERENCE_GENOME=/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa

BASE=/scratch/u035/project/trio_whole_exome/analysis
PARAMS_DIR=$BASE/params
READS_DIR=$BASE/reads
CONFIG_DIR=$BASE/config
WORK_DIR=$BASE/work
OUTPUT_DIR=$BASE/output

ARCHIVE_DIR=/archive/u035/trio_whole_exome

export PATH=/home/u035/project/software/bcbio/tools/bin:$PATH