/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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/airrflow -profile test_maskprimers_align,<docker/singularity> --outdir <OUTDIR>

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

params {
    config_profile_name        = 'Test maskprimers align'
    config_profile_description = 'Minimal test dataset to check pipeline function'

    // Input data
    input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv'
    cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'
    vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta'
    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

    mode = 'fastq'

    library_generation_method = 'specific_pcr_umi'
    cprimer_position = 'R1'
    umi_length = 8
    umi_start = 6
    umi_position = 'R1'
    index_file = true
    maskprimers_align = true
}
