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

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


aws.client.downloadParallel = true


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

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

    input  = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/samplesheet/samplesheet.csv"
    input_basedir  = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/testdata"

    multiplet_recovery = true
    min_size = 2
    max_size = 100000
    compute_polarization = true
    use_full_bipartite = true
    colocalization_min_region_count = 0
    colocalization_n_permutations = 10
    colocalization_neighbourhood_size = 1
}
