poxmvp_clinical_params.yaml

prefix: "poxmvp-reference"
mode: "reference"
grouping_criteria: "lineage"
skip_classification: true
skip_postprocessing: false
skip_posting: true
skip_harmonize: false
skip_peptide_annottaion: true
start_date: "2000-01-01"
end_date: "2025-01-20"
metadata_source: "Pathoplexus_mpox"
metadata_config: "assets/metadata_conf/metadata_mpox.yaml"
outdir: "results/poxmvp"
virus_accession_id: "NC_063383.1"
maxns: 3940
minlength: 197000
funcannot: "assets/virus_functionalAnnotation/NC_063383.1/Pokay_functionalAnnotation_MPOX_v1.0.tsv"
genecoord: "assets/virus_geneCoordinates/NC_063383.1/NC_063383.1.json"
surveillance_indicators: "assets/virus_surveillanceIndicators/functions_df_template.tsv"
viral_gbk: "assets/virus_genomeFeatures/NC_063383.1/NC_063383.1.gbk"
viral_gff: "assets/virus_genomeAnnotation/NC_063383.1/NC_063383.1.gff"
viral_genome: "assets/virus_referenceGenome/NC_063383.1/NC_063383.1.fasta"
viral_genome_fai: "assets/virus_referenceGenome/NC_063383.1/NC_063383.1.fasta.fai"
variant: "assets/virus_variants/NC_063383.1/variants_classification.tsv"
meta: "test_data/mpox/mpox_test_data.tsv.gz"
seq: "test_data/mpox/mpox_test_data.fa.gz"