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

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

stubRun = true
params {
    config_profile_name         = 'Test AmpliconArchitect profile'
    config_profile_description  = 'Test AmpliconArchitect functionality'

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

    // Input data
    input   = 'https://raw.githubusercontent.com/nf-core/test-datasets/circdna/samplesheet/samplesheet.csv'

    // Outdir
    outdir      = "./results"

    // Genome references
    fasta               = 'https://raw.githubusercontent.com/nf-core/test-datasets/circdna/reference/genome.fa'
    circle_identifier   = 'ampliconarchitect'
    skip_markduplicates = true
    igenomes_ignore     = true

    cnvkit_cnn		= "https://raw.githubusercontent.com/nf-core/test-datasets/circdna/cnvkit/dummy_file.cnn"
    mosek_license_dir   = "https://raw.githubusercontent.com/nf-core/test-datasets/circdna/mosek/mosek.lic"
    aa_data_repo        = "data_repo"
    reference_build     = "GRCh38"
    skip_qc             = true
}
