test.config

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

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

process {
    resourceLimits = [
        cpus: 4,
        memory: '15.GB',
        time: '1.h'
    ]
}

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

    // Input data
    primer_fwd = "GTGYCAGCMGCCGCGGTAA"
    primer_rev = "GGACTACNVGGGTWTCTAAT"
    input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_v3.tsv"
    metadata = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Metadata.tsv"
    dada_ref_taxonomy = "gtdb=R07-RS207"
    cut_dada_ref_taxonomy = true
    qiime_ref_taxonomy = "greengenes85"

    // ASV generation
    sample_inference = "independent"

    // ASV postprocessing
    vsearch_cluster = true
    decontam = "decontaminate"
    filter_ssu = "bac"
    max_len_asv = 255

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

    //produce average barplots
    metadata_category_barplot = "treatment1"

    //restrict ANCOM analysis to higher taxonomic levels
    tax_agglom_max = 2

    sbdiexport = true
    qiime_adonis_formula = "treatment1,mix8"
    diversity_rarefaction_depth = 500

    // Test ANCOMBC
    ancombc = true
    ancombc_formula = "treatment1"
    ancombc_formula_reflvl = "treatment1::b"
    ancombc_effect_size = 2
    ancombc_significance = 0.00001

    // Test ANCOMBC2
    ancombc2 = true
    ancombc2_formula = "treatment1"
    ancombc2_formula_reflvl = "treatment1::b"
}