#!/bin/bash

umask 007 # permissions for all files; group + user all rw, no outside user access

# This file contains paths and settings to be used by all bash scripts in the pipeline

# this should be 'source'd

#~~~~~ DEFAULT LOCATIONS & ITEMS ~~~~~~#

# path to output directory

outdir="output"

# path to code dir

codedir="code"

samplesheet_dir="samplesheets"

# path to report templates directory

report_template_dir="report"

# file for per sample full report template

full_report_template="${report_template_dir}/full_report.Rmd"

# file for the overall analysis full report

overview_report_template="${report_template_dir}/overview_report.Rmd"

# file containing list of actionable genes

actionable_genes_file="data/actionable_genes.txt"

# list of canonical transcripts to use; one per line

transcr_file="ref/hg19/canonical_transcript_list.txt"

# genes in the panel

panel_genes_file="data/panel_genes.txt"

# file with server login information

server_info_file="data/server_info.txt"

# file with extended regex NC sample ID's

control_sample_regex_file="data/control_sample_regex.txt"

# file with control sample ID's

control_sample_ID_file="data/control_sample_IDs.txt"

# file with SC control sample ID's to be hidden in report template

SC_control_sample_IDs_file="data/SC_control_sample_IDs.txt"

#~~~~~ CUSTOM FUNCTIONS ~~~~~~#

if [ -f "${codedir}/custom_bash_functions.sh" ]; then

source "${codedir}/custom_bash_functions.sh"

elif [ ! -f "${codedir}/custom_bash_functions.sh" ]; then

echo -e "ERROR: file not found:\n${codedir}/custom_bash_functions.sh"

echo -e "WARNING: Pipeline might not work correctly unless the file has been sourced from elsewhere"

fi

#~~~~~ DEFAULT SCRIPTS ~~~~~~#

compile_report_script="${codedir}/compile_RMD_report.R"

# ~~~~~~ ANNOTATION PARAMETERS ~~~~~~ #

# ANNOVAR version:

# Version: $Date: 2015-06-17 21:43:53 -0700 (Wed, 17 Jun 2015) $

build_version="hg19"

annovar_db_dir="$(readlink -f bin/annovar/db)"

convert2annovar_bin="$(readlink -f bin/annovar/convert2annovar.pl)"

table_annovar_bin="$(readlink -f bin/annovar/table_annovar.pl)"

annovar_protocol="-protocol refGene,cosmic68,clinvar_20150629,1000g2015aug_all -operation g,f,f,f"

# bcftools-1.3.1

bcftools_bin="$(readlink -f bin/bcftools)"

vcf2tsv_bin="$(readlink -f bin/vcf2tsv)"

# ~~~~~~ REMOTE IONTORRENT SERVER LOCATION NAMES AND PATTERNS ~~~~~~ #

# e.g. a path to remote IT server results looks like this:

# /results/analysis/output/Home/Auto_user_SN2-282-IT17-26-1_375_368/plugin_out/coverageAnalysis_out.1070/IonXpress_001

# ^^ this is the coverage output dir (.bam, .bai) for a single sample

# /results/analysis/output/Home/Auto_user_SN2-282-IT17-26-1_375_368/plugin_out/variantCaller_out.1071/IonXpress_001

#

# ^^ this is the coverage output dir (.vcf) for a single sample

# path to the 'Home' directory on the IonTorrent remote server that holds the

# run output results

IT_server_results_home_dir="/results/analysis/output/Home/"

# subdir name prefix for IT results dir that hold the coverege files for all samples; .bam and .bai files

IT_coverage_dir_name_pattern="coverageAnalysis_out"

# same but for the variant calling output

IT_variant_dir_name_pattern="variantCaller_out"

# subdir basename pattern for each sample on the IonTorrent output coverage and variant dirs

IT_sample_results_dir_name_pattern="IonXpress"

# source VCF file name on the remote IonTorrent server: TSVC_variants.vcf

source_vcf_basename="TSVC_variants.vcf"

# ~~~~~~~~~~~~ # file extensions & naming # ~~~~~~~~~~~~ #

# split VCF extensions

split_vcf_ext=".split"

# ANNOVAR converted avinput

avinput_ext=".avinput"

# ANNOVAR annotated output; automatically added by ANNOVAR

annovar_output_ext=".${build_version}_multianno.txt" # .hg19_multianno.txt

# rebuilt VCF file from ANNOVAR avinput

rebuilt_ext=".rebuilt"

# VCF field query tables

query_ext="_query.tsv"

# VCF converted to TSV

tsv_ext=".tsv"

## NOTE: These are hardcoded in merge_vcf_annotations.py

# variant summary table

summary_table_ext="_summary.tsv"

# variant table without summary criteria (not actually filtered why is it called that??)

filtered_table_ext="_filtered.tsv"

# full table with all variants and all fields

full_table_ext="_full_table.tsv"

# summary table with version control information

summary_version_ext="_summary_version.tsv"

# current_date="$(date +%Y-%m-%d:%H:%M:%S)"

# ~~~~~~ REPORTING PARAMETERS ~~~~~~ #

# if the 'module' system is installed, try to load the correct versions

if (module)&>/dev/null ; then

module unload r

module load r/3.3.0

module load pandoc/1.13.1

else

echo "WARNING: 'module' system not found, R and pandoc were not loaded automatically"

fi