/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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/proteinfamilies -profile test_minimal,<docker/singularity> --outdir <OUTDIR>

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

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

params {
    config_profile_name        = 'Minmal test profile'
    config_profile_description = 'Minimal test dataset to check pipeline function (no MSA clipping, no redundancy checking, no update)'

    // Input data
    input                               = params.pipelines_testdata_base_path + 'samplesheets/samplesheet.csv'
    // QC
    skip_preprocessing                  = true
    // Clustering
    clustering_tool                     = 'linclust'
    cluster_seq_identity                = 0.5
    cluster_coverage                    = 0.9
    cluster_size_threshold              = 5
    // Alignment
    skip_msa_trimming                   = true
    skip_additional_sequence_recruiting = true
    // Redundancy
    skip_family_redundancy_removal      = true
    skip_family_merging                 = true
    skip_sequence_redundancy_removal    = true
}
