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

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

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   = 8
    max_memory = '6.GB'
    max_time   = '6.h'

    // Input data
    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
    // TODO nf-core: Give any required params for the test so that command line flags are not needed
    input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
    databases           = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
    run_kraken2         = true
    run_malt            = true
    shortread_clipmerge = true

}

process {
    withName: FASTQC {
        cpus   = { check_max( 8     * task.attempt, 'cpus'    ) }
        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
        time   = { check_max( 6.h   * task.attempt, 'time'    ) }
    }
    withName: FASTQC_PROCESSED {
        cpus   = { check_max( 8     * task.attempt, 'cpus'    ) }
        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
        time   = { check_max( 6.h   * task.attempt, 'time'    ) }
    }
}