test_contamination.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,<docker/singularity> --outdir <OUTDIR>

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

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

    // Input data

    input            = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet.csv'
    fasta            = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa'

    mirtrace_species         = 'hsa'
    skip_mirdeep             = true
    save_merged              = false


    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'