covidmvp_wastewater_params.yaml

prefix: "covidmvp-wastewater"
gene_alias: "assets/virus_genomeAnnotation/NC_045512.2/NC_045512.2_key.json"
mode: "wastewater"
input: "test_data/sars-cov-2/wastewater/samplesheet.csv"
wastewater: true
skip_dehosting: true
skip_postprocessing: false
skip_posting: true
outdir: "results/covidmvp/wastewater"
viral_aligner: "bwa"
dehost_aligner: "bwa"
skip_variantannotation: true
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"