#!/bin/bash --login

module load apps/gcc/R/4.1.2

script_dir=${1}
name=${2}
input_dir=${3}
output_dir=${4}
wgd_file=${5}
file_pattern=${6}
sample_list=${7}

if [ "${sample_list}" != "" ]; then
  sample_list_text="sample_list=${sample_list}"
fi

# NOTE: file_pattern may need to be altered depending on the suffix of your copy number segment files (e.g. Battenberg outputs)
echo "Running step 1"
Rscript ${script_dir}/TM_1_collate_all_subclone_files_CW.R ${name} file_pattern=${file_pattern} input_dir=${input_dir} output_dir=${output_dir} ${sample_list_text}

echo "Running step 2"
Rscript ${script_dir}/TM_2_CNA_logic_CW.R ${name} input_dir=${output_dir}/ output_dir=${output_dir}/ wgd_file=${wgd_file}