chore: remove template RUNS/ directory

RUNS/COPY_ENTIRE_JOB_DIRECTORY_FOR_EACH_RUN

RUNS/JOB/cluster.json

RUNS/JOB/input_files/samples_table.csv

RUNS/JOB/map/cluster.json

RUNS/JOB/map/config.yaml

RUNS/JOB/map/intermediate_files.txt

RUNS/JOB/map/run_workflow_local.sh

RUNS/JOB/map/run_workflow_slurm.sh

RUNS/JOB/prepare/cluster.json

RUNS/JOB/prepare/config.yaml

RUNS/JOB/prepare/run_workflow_local.sh

RUNS/JOB/prepare/run_workflow_slurm.sh

RUNS/JOB/quantify/cluster.json

RUNS/JOB/quantify/config.yaml

RUNS/JOB/quantify/run_workflow_local.sh

RUNS/JOB/quantify/run_workflow_slurm.sh

RUNS/JOB/run_workflow_local.sh

RUNS/JOB/run_workflow_slurm.sh