covidmvp_timeseries_params.yaml

prefix: "covidmvp-2024-04-30-3months"
mode: "reference"
grouping_criteria: "time"
viralai: false
virusseq: true
virusseq_update: false
skip_classification: true
skip_postprocessing: true
skip_harmonize: true
start_date: "2020-01-01"
end_date: "2020-04-01"
metadata_source: "ViralAi_EpiCoV"
metadata_config: "assets/metadata_conf/metadata_ncov.yaml"
outdir: "results/covidmvp"
meta: "test_data/sars-cov-2/sars-cov-2-test-reference-metadata.tsv.gz"
seq: "test_data/sars-cov-2/sars-cov-2-test-reference-seq.fa.gz"
virus_accession_id: "NC_045512.2"
probvcf: "assets/virus_problematicSites/NC_045512.2/problematic_sites_sarsCov2.vcf"
funcannot: "assets/virus_functionalAnnotation/NC_045512.2/Pokay_functionalAnnotation_SARSCoV2_v4.2.tsv"
surveillance_indicators: "assets/virus_surveillanceIndicators/functions_df_template.tsv"
genecoord: "assets/virus_geneCoordinates/NC_045512.2/NC_045512.2.json"
mutationsplit: "assets/ncov_multiNames/mutation_names_to_split.tsv"
viral_gbk: "assets/virus_genomeFeatures/NC_045512.2/NC_045512.2.gbk"
viral_gff: "assets/virus_genomeAnnotation/NC_045512.2/NC_045512.2.gff"
viral_genome: "assets/virus_referenceGenome/NC_045512.2/NC_045512.2.fasta"
viral_genome_fai: "assets/virus_referenceGenome/NC_045512.2/NC_045512.2.fasta.fai"