params {
    config_profile_name        = 'Test PEP profile'
    config_profile_description = 'Minimal test dataset to check pipeline function with PEP file as an input.'

    // Limit resources so that this can run on GitHub Actions
    max_cpus   = 2
    max_memory = '6.GB'
    max_time   = '6.h'

    // Input data
    input                                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml'
    databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
    perform_shortread_qc                  = true
    perform_longread_qc                   = true
    perform_shortread_complexityfilter    = true
    perform_shortread_hostremoval         = true
    perform_longread_hostremoval          = true
    perform_runmerging                    = true
    hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
    run_kaiju                             = true
    run_kraken2                           = true
    run_bracken                           = true
    run_malt                              = true
    run_metaphlan3                        = true
    run_centrifuge                        = true
    run_diamond                           = true
    run_motus                             = false
    run_krona                             = true
    krona_taxonomy_directory              = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
    malt_save_reads                       = true
    kraken2_save_reads                    = true
    centrifuge_save_reads                 = true
    diamond_save_reads                    = true
}


process {
    withName: MALT_RUN {
        maxForks = 1
        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
    }
    withName: MEGAN_RMA2INFO {
        maxForks = 1
    }
}