test_prokka.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/funcscan -profile test_prokka,<docker/singularity> --outdir <OUTDIR>

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

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

params {
    config_profile_name        = 'AMP/ARG Prokka test profile'
    config_profile_description = 'Minimal test dataset to check pipeline function'

    // Input data
    input                      = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'

    annotation_tool            = 'prokka'

    run_arg_screening          = true
    arg_fargene_hmmmodel       = 'class_a,class_b_1_2'

    run_amp_screening          = true
    amp_run_hmmsearch          = true
    amp_hmmsearch_models       = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
}