config-Ubuntu.yml

###############################################################################
#
#   Config options for the snakemake workflow
#
#   AUTHOR: Maciej_Bak
#   CONTACT: wsciekly.maciek@gmail.com
#   CREATED: 15-02-2022
#   LICENSE: Apache_2.0
#
###############################################################################
---

### WORKFLOW PARAMETERS ###

# Path to the cloned repository
# (absolute path is required, also: do not use "~" character -
# some HPC clusters evaluate it differently on login & computing nodes)
workflow_repo_path: "/home/runner/work/warlock/warlock"

# Path for the output directory
# (absolute path is required, also: do not use "~" character -
# some HPC clusters evaluate it differently on login & computing nodes)
workflow_analysis_outdir: "/home/runner/work/warlock/warlock/tests/test2/output"

### DEMON PARAMETERS ###

# spatial_structure
demon_log2_deme_carrying_capacity: [1, 2, 3, 4]

# dispersal
demon_migration_type: 0
demon_init_migration_rate: "2e-03"
demon_migration_edge_only: 1
demon_migration_rate_scales_with_K: 1

# mutation_rates
demon_mu_driver_birth: "1e-05"
demon_mu_passenger: 0.001
demon_mu_driver_migration: 0.001
demon_passenger_pop_threshold: -1

# fitness_effects
demon_normal_birth_rate: [0.8, 0.82, 0.84, 0.86, 0.88, 0.9]
demon_baseline_death_rate: 0
demon_s_driver_birth: 0.1
demon_s_passenger: 0
demon_s_driver_migration: 0
demon_max_relative_birth_rate: 10
demon_max_relative_migration_rate: 10

# non_biological_parameters
demon_init_pop: 1
demon_matrix_max: -1
demon_max_pop: 10000
demon_max_time: 86400
demon_max_generations: 2000
demon_seed: 10
demon_write_grid: 0
demon_write_clones_file: 0
demon_write_demes_file: 0
demon_record_matrix: 0
demon_write_phylo: 0
demon_calculate_total_diversity: 0
demon_biopsy_size_per_sample: 100

...