/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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 = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/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'
    imgtdb_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
    igblast_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'

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

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