/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Nextflow config file for running minimal tests (LFQ)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Defines input files and everything required to run a fast and simple test.

    Use as follows:
        nextflow run nf-core/quantms -profile test_lfq,<docker/singularity> [--outdir <OUTDIR>]

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

params {
    config_profile_name        = 'Test profile for DDA LFQ'
    config_profile_description = 'Minimal test dataset to check pipeline function of the label-free quantification branch of the pipeline'

    // Limit resources so that this can run on GitHub Actions
    max_cpus = 2
    max_memory = 6.GB
    max_time = 48.h

    outdir = "./results_lfq"
    tracedir = "${params.outdir}/pipeline_info"

    // Input data
    labelling_type = "label free sample"
    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci/BSA/BSA_design_urls.tsv'
    database = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci/BSA/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta'
    posterior_probabilities = "fit_distributions"
    search_engines = "msgf,comet"
    decoy_string= "rev"
    add_triqler_output = true
    protein_level_fdr_cutoff = 1.0
    psm_level_fdr_cutoff = 1.0
    acquisition_method = "dda"
    quantify_decoys = true
}
