/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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_pplace,<docker/singularity> --outdir <OUTDIR>

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

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

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

    // Input data
    FW_primer = "GTGYCAGCMGCCGCGGTAA"
    RV_primer = "GGACTACNVGGGTWTCTAAT"
    input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet.tsv"
    metadata = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Metadata.tsv"
    skip_dada_taxonomy = true
    qiime_ref_taxonomy = "greengenes85"
    filter_ssu = "bac"

    // this is to remove low abundance ASVs to reduce runtime of downstream processes
    min_samples = 2
    min_frequency = 10

    // pplace
    pplace_tree = params.pipelines_testdata_base_path + "phyloplace/testdata/cyanos_16s.newick"
    pplace_aln = params.pipelines_testdata_base_path + "phyloplace/testdata/cyanos_16s.alnfna"
    pplace_model = "GTR+F+I+I+R3"
    pplace_taxonomy = params.pipelines_testdata_base_path + "phyloplace/testdata/cyanos_16s.taxonomy.tsv"
    pplace_name = "test_pplace"

    // Adjust taxonomic levels
    tax_agglom_min = 1
    tax_agglom_max = 3

    // Skip some steps to reduce runtime
    skip_alpha_rarefaction = true
    skip_fastqc = true
}
