input_dir=path/to/directory_with_Battenberg_outputs/
required_files_dir=path/to/direcory_with_other_required_files/
output_dir=path/to/output_dir/
name=name_of_dataset_and_run
TM_dir=another/path/to/Timing_Model/

# Run ordering model in de novo discovery mode using PLMIX
${TM_dir}/BASH/pipeline.sh -n ${name} -i ${input_dir} -o ${output_dir} -p PLMIX -g 1,2,3,4,5 -u notIncluded -r ${required_files_dir}/driver_gene_list.txt -m ${required_files_dir}/nonsynonymous_muts.txt -d ${required_files_dir}/dpclust_data/ -w ${required_files_dir}/dataset_wgd_status.txt -s ${required_files_dir}/selected_samples_list.txt -a hg38 -c ${required_files_dir}/WCC_bestClusterInfo/

# Discover the number of subgroups
qsub ${TM_dir}/BASH/run_postFDR_5b.sh ${TM_dir}/R/TM_postFDR_5b_select_best_G.R PPCG_selected_primary_samples ${PPCG_dir}/${name}/

# For each of the de novo discovered subgroups, run the final ordering model with PlackettLuce, e.g.
for dn in 1 2 3; do
  name=${name}_DN${dn}
  ${TM_dir}/BASH/pipeline.sh -n ${name} -i ${input_dir} -o ${output_dir} -p PlackettLuce -g 1 -u notIncluded -r ${required_files_dir}/driver_gene_list.txt -m ${required_files_dir}/nonsynonymous_muts.txt -d ${required_files_dir}/dpclust_data/ -w ${required_files_dir}/dataset_wgd_status.txt -s ${required_files_dir}/selected_samples_list.txt -a hg38 -c ${required_files_dir}/WCC_bestClusterInfo/
done