/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Nextflow config file for running full-size tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Defines input files and everything required to run a full size pipeline test.

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

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

params {
    config_profile_name = 'Full test profile'
    config_profile_description = 'Full test dataset to check pipeline function'

    // Input data for full size test
    FW_primer = "GTGYCAGCMGCCGCGGTAA"
    RV_primer = "GGACTACNVGGGTWTCTAAT"
    input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_full.tsv"
    metadata = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Metadata_full.tsv"
    dada_ref_taxonomy = "rdp"
    qiime_ref_taxonomy = "greengenes85"
    trunc_qmin = 35

    //this is to remove very low abundance and low prevalence ASVs to reduce runtime of downstream processes
    min_samples = 3
    min_frequency = 30

    //produce average barplots
    metadata_category_barplot = "habitat"

    //run Picrust2
    picrust = true

    //run adonis
    qiime_adonis_formula = "habitat"

    //run ANCOM & ANCOMBC
    ancom = true
    ancombc = true
}
