/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Nextflow config file for running full-size tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Defines input files and everything required to run a full size pipeline test.

    Use as follows:
        nextflow run nf-core/airrflow -profile test_full,<docker/singularity> --outdir <OUTDIR>

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

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

    // Input data
    input = pipelines_testdata_base_path + 'testdata-bcr/metadata_pcr_umi_airr_300.tsv'
    cprimers = 's3://ngi-igenomes/test-data/airrflow/pcr_umi/cprimers.fasta'
    vprimers = 's3://ngi-igenomes/test-data/airrflow/pcr_umi/vprimers.fasta'
    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

    lineage_trees = true

    // Other params
    library_generation_method = 'specific_pcr_umi'
    cprimer_position = 'R1'
    umi_length = 15
    umi_start = 0
    umi_position = 'R1'
    isotype_column = 'c_primer'
}

process {
    withName:DOWSER_LINEAGES{
        ext.args = ['minseq':5,
                    'traits':'isotype',
                    'tips':'isotype']
    }

    withName:DEFINE_CLONES_COMPUTE{
        ext.args = ['outname':'', 'model':'hierarchical',
                    'method':'nt', 'linkage':'single',
                    'min_n':30]

    }
    withName:DEFINE_CLONES_REPORT{
        ext.args = ['outname':'', 'model':'hierarchical',
                    'method':'nt', 'linkage':'single',
                    'min_n':30]

    }
}
