config.yaml

#########################################################
# Complete one of the following input data
# Remove the other lines if not needed
#########################################################

# Genbank accessions of assembly accession (GCA, GCF)
ids:
  - GCA_001042775.1
  - GCA_001021915.1
  - GCA_022406815.1

# Path of genbank files
input_genbanks:
  - data/GCA_001518895.1.gb
  - data/GCA_001746615.1.gb
  - data/GCA_003382895.1.gb

# Input genomes as fasta and annotation files in GFF format
# Only applied when using Orthofinder or PGGB workflows, starting from fasta and GFF
# To be used preferentially for eukaryotes
input_genomes:
  "MSU7":
    "fasta": "/share/banks/Oryza/sativa/japonica/MSU7/all.con"
    "gff3": "/share/banks/Oryza/sativa/japonica/MSU7/all.gff3"
    "name": "MSU7"
  "kitaake":
    "fasta": "/share/banks/Oryza/sativa/japonica/kitaake/Oryza_sativa_japonica_Kitaake.assembly.fna"
    "gff3": "/share/banks/Oryza/sativa/japonica/kitaake/Oryza_sativa_japonica_Kitaake.gff3"
    "name": "kitaake"
  "nivara":
    "fasta": "/share/banks/Oryza/nivara/Oryza_nivara.assembly.fna"
    "gff3": "/share/banks/Oryza/nivara/Oryza_nivara.gff3"
    "name": "nivara"

identity: 80