TreeVal.yaml

assembly:
  level: scaffold
  sample_id: Oscheius_DF5033
  latin_name: to_provide_taxonomic_rank
  classT: nematode
  asmVersion: 1
  gevalType: DTOL
reference_file: /Users/dp24/Documents/FastaManipulator/TreeValTestDir/assembly/test.fasta
assem_reads:
  pacbio: /Users/dp24/Documents/FastaManipulator/TreeValTestDir/genomic_data/pacbio/fasta/
  hic: /Users/dp24/Documents/FastaManipulator/TreeValTestDir/genomic_data/hic-arima2/
  supplementary: path
alignment:
  data_dir: /Users/dp24/Documents/FastaManipulator/TreeValTestDir/gene_alignment_data/
  common_name: "" # For future implementation (adding bee, wasp, ant etc)
  geneset: "OscheiusTipulae.ASM1342590v1,CaenorhabditisElegans.WBcel235,Gae_host.Gae"
  #Path should end up looking like "{data_dir}{classT}/{common_name}/csv_data/{geneset}-data.csv"
self_comp:
  motif_len: 0
  mummer_chunk: 10
intron:
  size: "50k"
telomere:
  teloseq: TTAGGG
synteny:
  synteny_genome_path: /Users/dp24/Documents/FastaManipulator/TreeValTestDir/synteny/
busco:
  lineages_path: /Users/dp24/Documents/FastaManipulator/TreeValTestDir/busco/v5
  lineage: nematoda_odb10