nextflow.config

manifest {
    author                            = 'John Arnn'
    defaultBranch                     = 'main'
    description                       = 'A a real-time snapshot of evolving pathogen populations necessitates a reproducible analysis that can be rerun when new sequences are available.'
    homePage                          = 'https://github.com/UPHL-BioNGS/Nextstrain_Build'
    mainScript                        = 'main.nf'
    name                              = 'NextStrain'
    version                           = 'TBD'
}

profiles {
    docker {
        docker.enabled                = true
        docker.runOptions             = "-u \$(id -u):\$(id -g) --user root"
    }
    singularity {
       singularity.enabled            = true
        singularity.autoMounts        = true 
    }
    test {
        docker.enabled                = true
        docker.runOptions             = "-u \$(id -u):\$(id -g)"
        params.multi_fasta            = './data/sequences.fasta'
        params.metadata               = './data/metadata.tsv'
        params.dropped_strains        = './data/dropped_strains.txt'
        params.outgroup               = './data/zika_outgroup.gb'
        params.group_by               =  'country year month'
        params.sequences_per_group    =  '20'
        params.min_date               =  '2012'
        params.fill_gaps              = true
        params.date_confidence        = true
        params.timetree               = true
        params.coalescent             = 'opt'
        params.date_inference         = 'marginal'
        params.clock_filter_iqd       = '4'
        params.indentify_aa_mutations = true
        params.columns                = '[region country]'
        params.confidence             = true
        params.inference              = 'joint'
        params.colors                 = './data/colors.tsv'
        params.lat_longs              = './data/lat_longs.tsv'
        params.auspice_config         = './data/auspice_config.json'
    }
}

includeConfig './configs/template.config'