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

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

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

params {
    config_profile_name = 'Test custom DADA2 reference taxonomy database profile'
    config_profile_description = 'Minimal test dataset to check --dada_ref_tax_custom'

    // Input data
    FW_primer = "GTGYCAGCMGCCGCGGTAA"
    RV_primer = "GGACTACNVGGGTWTCTAAT"
    input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet.tsv"

    // Custom reference taxonomy
    dada_ref_tax_custom = "https://zenodo.org/record/4310151/files/rdp_train_set_18.fa.gz"
    dada_ref_tax_custom_sp = "https://zenodo.org/record/4310151/files/rdp_species_assignment_18.fa.gz"
    dada_assign_taxlevels = "Kingdom,Phylum,Class,Order,Family,Genus"
    kraken2_ref_tax_custom = "https://genome-idx.s3.amazonaws.com/kraken/16S_Greengenes13.5_20200326.tgz"
    kraken2_assign_taxlevels = "D,P,C,O"
    qiime_ref_tax_custom = params.pipelines_testdata_base_path + "ampliseq/testdata/85_greengenes.tar.gz"

    // Skip downstream analysis with QIIME2
    skip_qiime_downstream = true
}
