config.yml

threads: 64
reference_genome: reference_genome.fasta
primer_scheme: V4
scheme_dir: primer_schemes
seed: 2022
container_directory: singularity
nextflow_path: /hps/nobackup/iqbal/dander/viridian_simulations_workflow/nextflow

phastSim:
  tree_file: newick_output.nwk
  output_dir: phastSim_output
  rate_parameter: 1

split_amplicons:
  random_dropout_probability: 0.001
  primer_dimer_probability: 0.001
  match_coverage_mean: 500
  match_coverage_sd: 20
  mismatch_coverage_mean: 0
  mismatch_coverage_sd: 0

simulate_reads:
  illumina_read_length: 250

artic_assemble:
  scheme_url: https://github.com/artic-network/primer-schemes
  main_nf: singularity/ncov2019-artic-nf/main.nf
  illumina_workflow_container: singularity/ncov2019-artic-nf/artic-ncov2019-illumina.sif

epi2me_badread_assemble:
  main_nf: /nfs/research/zi/mhunt/Covid/Epi2me/wf-artic/main.nf
  nxf_sing_cache: /hps/nobackup/iqbal/dander/viridian_simulations_workflow/singularity/epi2me/nf_cache

mask_assemblies:
  apply_mask: False

viridian_assemble:
  viridian_container: /nfs/research/zi/mhunt/Containers/viridian_workflow_v1.1.0.img