/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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/nascent -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   = 2
    max_memory = '6.GB'
    max_time   = '6.h'

    // Input data
    input = "${projectDir}/assets/samplesheet.csv"

    // Genome references
    fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21.fa'
    gtf = 's3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf'

    assay_type = "GROseq"
    skip_grohmm = true // FIXME Fails due to higher memory requirements
    tuning_file = "${projectDir}/tests/subworkflows/local/grohmm/tuningparams_small.csv"
    filter_bed = "${projectDir}/tests/samplesheets/region.bed"
}

process {
    // FIXME https://github.com/hyulab/PINTS/issues/12
    withName: PINTS_CALLER {
        ext.when = false
    }
}
