# This configuration file should contain all required configuration parameters
# for the Nextclade workflow to run to completion.
#
# Define optional config parameters with their default values here so that users
# do not have to dig through the workflows to figure out the default values

strain_id_field: "accession"
display_strain_field: "strain"

inputs:
  - name: ncbi
    sequences: "https://data.nextstrain.org/files/workflows/lassa/all/sequences.fasta.zst"
    metadata: "https://data.nextstrain.org/files/workflows/lassa/all/metadata.tsv.zst"

gpc_manual_alignment: "https://raw.githubusercontent.com/JoiRichi/LASV_ML_manuscript_data/main/alignment_preprocessing/final_passed_sequences_manual_curated.fasta"

segments: ['gpc', 'l', 's']

clade_membership:
  metadata: "defaults/{segment}/metadata_clade_membership.tsv"
  fallback: "{segment}_lineage"

filter:
  gpc: '--exclude-all'
  l: '--exclude-all'
  s: '--exclude-all'

tree:
  method: "iqtree"

refine:
  gpc: '--root ROOT_UNCLASSIFIED'
  l: '--root mid_point'
  s: '--root mid_point'

ancestral:
  inference: "joint"

traits:
  columns: "clade_membership"

export:
  auspice_config: "defaults/auspice_config.json"
  description: "../phylogenetic/defaults/description.md"
