nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/detaxizer Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {

    // Input options
    input                      = null

    // References
    genome                     = 'GRCh38'
    igenomes_base              = 's3://ngi-igenomes/igenomes/'
    igenomes_ignore            = false

    saveReference              = true
    fasta_blastn               = null
    fasta_bbduk                = null

    // Workflow parameters
    preprocessing                           = false
    skip_filter                             = false
    filter_trimmed                          = false
    output_removed_reads                    = false
    filtering_tool                         = 'seqkit'
    classification_kraken2                  = false
    classification_bbduk                    = false
    validation_blastn                       = false
    filter_with_classification              = false
    classification_kraken2_post_filtering   = false
    save_intermediates                      = false

    // fastp parameter
    reads_minlength            = 0
    fastp_save_trimmed_fail    = false
    fastp_qualified_quality    = 0
    fastp_cut_mean_quality     = 1
    fastp_eval_duplication     = false
    save_clipped_reads         = false

    // bbduk parameter
    bbduk_kmers                = 27

    // Kraken2preparation parameter
    kraken2db                  = 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20240605.tar.gz'

    // Kraken2 parameter
    save_output_fastqs          = false
    save_output_fastqs_filtered = false
    save_output_fastqs_removed  = false
    kraken2confidence           = 0.00
    kraken2confidence_filtered  = 0.00
    kraken2confidence_removed   = 0.00
    // Taxon to check for/to filter in kraken2 format, it has to be present in the supplied kraken2 database
    tax2filter                 = 'Homo sapiens'
    // Parameters for the classification if a read is assigned to the taxa2filter or not
    cutoff_tax2filter          = 0
    cutoff_tax2keep            = 0.0
    cutoff_unclassified        = 0.0

    // BLASTN parameters
    blast_coverage             = 40.0
    blast_identity             = 40.0
    blast_evalue               = 0.01

    // Generate downstream samplesheets
    generate_downstream_samplesheets      = false
    generate_pipeline_samplesheets        = 'taxprofiler,mag'

    // MultiQC options
    multiqc_config             = null
    multiqc_title              = null
    multiqc_logo               = null
    max_multiqc_email_size     = '25.MB'
    multiqc_methods_description = null

    // Boilerplate options
    outdir                       = null
    publish_dir_mode             = 'copy'
    email                        = null
    email_on_fail                = null
    plaintext_email              = false
    monochrome_logs              = false
    hook_url                     = System.getenv('HOOK_URL')
    help                         = false
    help_full                    = false
    show_hidden                  = false
    version                      = false
    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')

    // Config options
    config_profile_name        = null
    config_profile_description = null

    custom_config_version      = 'master'
    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    config_profile_contact     = null
    config_profile_url         = null

    // Schema validation default options
    validate_params            = true
}

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

profiles {
    debug {
        dumpHashes              = true
        process.beforeScript    = 'echo $HOSTNAME'
        cleanup                 = false
        nextflow.enable.configProcessNamesValidation = true
    }
    conda {
        conda.enabled           = true
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        conda.channels          = ['conda-forge', 'bioconda']
        apptainer.enabled       = false
    }
    mamba {
        conda.enabled           = true
        conda.useMamba          = true
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    docker {
        docker.enabled          = true
        conda.enabled           = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
        docker.runOptions       = '-u $(id -u):$(id -g)'
    }
    arm64 {
        process.arch            = 'arm64'
        apptainer.ociAutoPull   = true
        singularity.ociAutoPull = true
        wave.enabled            = true
        wave.freeze             = true
        wave.strategy           = 'conda,container'
    }
    emulate_amd64 {
        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        singularity.enabled     = true
        singularity.autoMounts  = true
        conda.enabled           = false
        docker.enabled          = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    podman {
        podman.enabled          = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    shifter {
        shifter.enabled         = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    charliecloud {
        charliecloud.enabled    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        apptainer.enabled       = false
    }
    apptainer {
        apptainer.enabled       = true
        apptainer.autoMounts    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
    }
    wave {
        apptainer.ociAutoPull   = true
        singularity.ociAutoPull = true
        wave.enabled            = true
        wave.freeze             = true
        wave.strategy           = 'conda,container'
    }
    gpu {
        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
        apptainer.runOptions    = '--nv'
        singularity.runOptions  = '--nv'
    }
    test                        { includeConfig 'conf/test.config'                      }
    test_blastn                 { includeConfig 'conf/test_blastn.config'          }
    test_filter_preprocessed    { includeConfig 'conf/test_filter_preprocessed.config'  }
    test_full                   { includeConfig 'conf/test_full.config'                 }
}

// Load nf-core custom profiles from different institutions

// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
// Load nf-core/detaxizer custom profiles from different institutions.
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"


// Load nf-core/detaxizer custom profiles from different institutions.
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/detaxizer.config" : "/dev/null"

// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry    = 'quay.io'
docker.registry       = 'quay.io'
podman.registry       = 'quay.io'
singularity.registry  = 'quay.io'
charliecloud.registry = 'quay.io'

// Load igenomes.config if required
includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
    JULIA_DEPOT_PATH = "/usr/local/share/julia"
}

// Set bash options
process.shell = [
    "bash",
    "-C",         // No clobber - prevent output redirection from overwriting files.
    "-e",         // Exit if a tool returns a non-zero status/exit code
    "-u",         // Treat unset variables and parameters as an error
    "-o",         // Returns the status of the last command to exit..
    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
]

// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false

timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
    enabled = true
    file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}

manifest {
    name            = 'nf-core/detaxizer'
    contributors    = [
        // nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
        [
            name: 'Jannik Seidel',
            affiliation: 'Quantitative Biology Center (QBiC), University of Tübingen, Germany)',
            email: '',
            github: 'jannikseidelQBiC',
            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0009-0003-2867-2335'
        ],
        [
            name: 'Daniel Straub',
            affiliation: 'Quantitative Biology Center (QBiC), University of Tübingen, Germany)',
            email: '',
            github: 'd4straub',
            contribution: ['maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0002-2553-0660'
        ],
    ]
    homePage        = 'https://github.com/nf-core/detaxizer'
    description     = """A pipeline to identify and remove certain sequences from raw genomic data. Default taxon to identify and remove is Homo sapiens."""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=25.04.8'
    version         = '1.3.0'
    doi             = '10.5281/zenodo.10877147,10.1093/nargab/lqaf125'
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

validation {
    defaultIgnoreParams = ["genomes"]
    monochromeLogs = params.monochrome_logs
}

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'