/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Defines input files and everything required to run a fast and simple pipeline test.

    Use as follows:
        nextflow run nf-core/ampliseq -profile test_multiregion,<docker/singularity> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

process {
    resourceLimits = [
        cpus: 4,
        memory: '15.GB',
        time: '2.h'
    ]
}

params {
    config_profile_name = 'Test profile for multi-region analysis'
    config_profile_description = 'Test dataset to check multi-region pipeline function'

    // Input data
    input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/samplesheet_multiregion.tsv"
    metadata = params.pipelines_testdata_base_path + "ampliseq/samplesheets/metadata_multiregion.tsv"
    multiregion = params.pipelines_testdata_base_path + "ampliseq/samplesheets/regions_multiregion.tsv"
    sidle_ref_taxonomy = "greengenes88"

    // Prevent default taxonomic classification
    skip_dada_taxonomy = true

    // Reduce runtimes
    skip_alpha_rarefaction = true
    tax_agglom_max = 3

    // Run ANCOM
    ancom = true
}
