nextflow.config

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

// Global default params, used in configs
params {

    // Input options
    input           = null

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

    // FASTQ preprocessing
    skip_preprocessing_qc            = false
    preprocessing_qc_tool            = 'fastqc'

    perform_shortread_qc             = true
    shortread_qc_tool                = 'fastp'
    shortread_qc_skipadaptertrim     = false
    shortread_qc_mergepairs          = false
    shortread_qc_includeunmerged     = false
    shortread_qc_adapter1            = null
    shortread_qc_adapter2            = null
    shortread_qc_adapterlist         = null
    shortread_qc_minlength           = 50
    shortread_qc_dedup               = false

    perform_longread_qc                   = true
    longread_adapterremoval_tool          = 'porechop'
    longread_qc_skipadaptertrim           = false
    longread_qc_skipqualityfilter         = false
    longread_filter_tool                  = 'nanoq'
    longread_qc_qualityfilter_minlength   = 1000
    longread_qc_qualityfilter_keeppercent = 90
    longread_qc_qualityfilter_minquality  = 7
    longread_qc_qualityfilter_targetbases = 500000000

    save_preprocessed_reads          = false

    // run merging
    perform_runmerging          = true
    save_runmerged_reads        = true

    // Publishing final reads going into subsampling
    save_analysis_ready_fastqs = false

    // Subsampling
    perform_subsampling      = true
    subsampling_depth_cutoff = 100

    // Shortread mapping
    shortread_mapping_tool     = 'bowtie2'

    // Minimap2 options
    bam_format          =  true
    bam_index_extension = "bai"
    cigar_paf_format    = false
    cigar_bam           = true

    // clair3
    clair3_model    = ''
    clair3_platform = 'ont'

    // BCFtools consensus
    genomecov_scale = '1'
    genomecov_threshold = 9

    // Maximum non GATC bases (i.e - and N) to allow in pseudogenome sequences
    non_GATC_threshold         = 0.5

    // 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                     = null
    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)'
    }
    arm {
        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'
    }
    gitpod {
        executor.name           = 'local'
        executor.cpus           = 4
        executor.memory         = 8.GB
        process {
            resourceLimits = [
                memory: 8.GB,
                cpus  : 4,
                time  : 1.h
            ]
        }
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.config' }
}

// Load nf-core 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/bactmap custom profiles from different institutions.
// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/bactmap.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/bactmap'
    author          = """Andries J. van Tonder, Anthony Underwood, Than Le Viet and the nf-core/bactmap team""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
    contributors    = [
        [
            name: 'Andries J. van Tonder',
            affiliation: 'Department of Veterinary Medicine, University of Cambridge, Cambridge, UK',
            email: 'ajv37@cam.ac.uk',
            github: 'https://github.com/avantonder',
            contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: 'https://orcid.org/0000-0002-4380-5250'
        ],
        [
            name: 'Anthony Underwood',
            affiliation: 'Broken Strings Biosciences, Cambridge, UK',
            email: '',
            github: 'https://github.com/antunderwood',
            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: 'https://orcid.org/0000-0002-8547-4277'
        ],
        [
            name: 'Than Le Viet',
            affiliation: 'Quadram Institute, Norwich, UK',
            email: '',
            github: 'https://github.com/thanhleviet',
            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: 'https://orcid.org/0000-0002-2106-8130'
        ],
        [
            name: 'and the nf-core/bactmap team',
            affiliation: 'nf-core community',
            email: '',
            github: 'https://github.com/nf-core',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
    ]
    homePage        = 'https://github.com/nf-core/bactmap'
    description     = """A mapping-based pipeline for bacterial whole genome sequences"""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=25.10.0'
    version         = '2.0.0'
    doi             = ''
}

// 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'