/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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/nascent -profile test,<docker/singularity> --outdir <OUTDIR>

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

params {
    config_profile_name        = 'GROcap PINTS Test profile'
    config_profile_description = 'Test dataset to check PINTS pipeline function(https://pints.yulab.org/tre_calling#part-iii-case-1)'

    // Input data
    input = "${projectDir}/tests/samplesheets/grocap.csv"

    genome = 'hg38'
    assay_type = 'GROcap'
    filter_bed = "https://pints.yulab.org/ref/examples/promoters_1kb_tss_centered.bed.gz"
}

process {
    withName: NFCORE_NASCENT:NASCENT:FASTP {
        ext.args = [
            "--adapter_sequence TGGAATTCTCGGGTGCCAAGG",
            "-l 14", // only keep reads longer than 14nts after trimming
            // This library was polyadenylated,
            // so we are trimming the last 20nts per reads (with --trim_tail1).
            // For more recent single-end PRO/GRO-cap libraries, this may not be necessary.
            "--trim_tail1 20",
            "--low_complexity_filter",
            "-w 8"
        ].join(' ').trim()
    }
}
