/*
 * -------------------------------------------------
 *  Nextflow config file for running tests
 * -------------------------------------------------
 * Defines bundled input files and everything required
 * to run a fast and simple test. Use as follows:
 *   nextflow run nf-core/airrflow -profile test_tcr,<docker/singularity>
 */

params {
    config_profile_name = 'Test TCR'
    config_profile_description = 'Minimal test dataset to check pipeline function with TCR data'

    // Limit resources so that this can run on GitHub Actions
    max_cpus = 2
    max_memory = 6.GB
    max_time = 48.h

    // params
    mode = 'fastq'
    umi_length = 12
    umi_position = 'R2'
    cprimer_start = 5
    skip_report = false
    library_generation_method = 'dt_5p_race_umi'
    cprimer_position = 'R1'
    clonal_threshold = 0


    // Input data
    input = pipelines_testdata_base_path + 'testdata-tcr/TCR_metadata_airr.tsv'
    cprimers = pipelines_testdata_base_path + 'testdata-tcr/cprimers.fasta'
    race_linker = pipelines_testdata_base_path + 'testdata-tcr/linker.fasta'
    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

}

process{
    withName:"DEFINE_CLONES*"{
        ext.args = ['outname':'', 'model':'hierarchical',
                    'method':'nt', 'linkage':'single',
                    'outputby':'sample_id', 'min_n':10]
    }
}
