/*
========================================================================================
    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/cutandrun -profile test,<docker/singularity>

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

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

    // Limit resources so that this can run CI
    max_cpus   = 2
    max_memory = 6.GB
    max_time   = 6.h

    // Input data
    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet/test-GSE145187-small.csv'

    // Genome references
    fasta              = '/home/runner/work/cutandrun/cutandrun/hg38-chr20.fa.gz'
    bowtie2            = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-bowtie2.tar.gz'
    gtf                = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-genes.gtf.gz'
    gene_bed           = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-genes.bed.gz'
    blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
    spikein_fasta      = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.fa.gz'
    spikein_bowtie2    = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.tar.gz'

    minimum_alignment_q_score = 10
}