/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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/scdownstream -profile test_full,<docker/singularity> --outdir <OUTDIR>

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

process {
    resourceLimits = [
        cpus: 6,
        memory: '15.GB',
        time: '6.h'
    ]
}

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

    // Input data for full size test
    input                  = params.pipelines_testdata_base_path + 'samplesheet.csv'
    integration_methods    = 'scvi,symphony,bbknn,combat'
    doublet_detection      = 'solo,scrublet,doubletdetection,scdblfinder'
    celltypist_model       = 'Adult_Human_Skin'
    celldex_reference      = 'https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/singleR/references.csv'
    // CyteType calls a slow remote LLM API — covered by module nf-tests only
    cytetype_study_context = ''
    integration_n_features = 500
    feature_selection      = 'hvgs'
    scvi_max_epochs        = 5
}
