taxprofiler/conf/test_falcobbduk.config at b9a09b6ae6bf7b8835662a8293c2607c19b5fcc0 · nf-core/taxprofiler · GitHub

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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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_falcobbduk,<docker/singularity> --outdir <OUTDIR>

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

process {
    // Limit resources so that this can run on GitHub Actions
    resourceLimits = [
        cpus: 4,
        memory: '15.GB',
        time: '6.h',
    ]
}

params {
    config_profile_name                = 'Test profile for falco and bbduk'
    config_profile_description         = "Minimal test to falco and bbduk functionality in the short-read preprocessing steps"

    // Input data
    input                              = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_shortreadfastqpairsonly.csv'
    databases                          = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.3.csv'
    preprocessing_qc_tool              = 'falco'
    perform_shortread_qc               = true
    perform_longread_qc                = false
    perform_shortread_complexityfilter = true
    shortread_complexityfilter_tool    = 'bbduk'
    save_complexityfiltered_reads      = true
    perform_shortread_hostremoval      = true
    perform_longread_hostremoval       = false
    perform_runmerging                 = true
    hostremoval_reference              = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
    run_kaiju                          = true
    run_kraken2                        = true
    run_bracken                        = false
    run_malt                           = false
    run_metaphlan                      = false
    run_centrifuge                     = false
    run_diamond                        = false
    run_krakenuniq                     = false
    run_motus                          = false
    run_ganon                          = false
    run_kmcp                           = false
    run_sylph                          = false
    run_melon                          = false
}

process {
    withName: MALT_RUN {
        tag        = { "${meta.db_name}|${meta.id}" }
        maxForks   = 1
        ext.args   = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
        ext.prefix = { "${meta.db_name}" }
        publishDir = [
            path: { "${params.outdir}/malt/${meta.db_name}/" },
            mode: params.publish_dir_mode,
            pattern: '*.{rma6,log,sam}',
        ]
    }
    withName: NONPAREIL_NONPAREIL {
        ext.args   = { "-k 5" }
        ext.prefix = { "${meta.id}_${meta.run_accession}" }
        publishDir = [
            path: { "${params.outdir}/nonpareil/" },
            mode: params.publish_dir_mode,
            pattern: '*.np{a,c,l,o}',
        ]
    }
}