test_contamination_tech_reps.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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/smrnaseq -profile test_contamination_tech_reps,<docker/singularity> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/
// Test covers techincal_repeats, skip_fastqc, filter_contamination and running without genome.

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

    // Input data
    input      = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet_technical_repeats_short.csv'

    mirtrace_species         = 'hsa'
    save_intermediates       = true

    skip_multiqc             = true
    skip_mirdeep             = true
    skip_fastqc              = true

    filter_contamination     = true
    cdna                     = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/Homo_sapiens.GRCh37.cdna.all.fa"
    ncrna                    = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/Homo_sapiens.GRCh37.ncrna.fa"
    trna                     = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/hg19-tRNAs.fa"
}

// Include illumina config to run test without additional profiles

includeConfig 'protocol_illumina.config'