nextflow.config

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

// Global default params, used in configs
params {
    // Input options
    input                        = null
    peptide_col_name             = 'sequence'
    peptides_split_maxchunks     = 100
    peptides_split_minchunksize  = 5000
    split_by_variants            = false
    split_by_variants_size       = 0
    split_by_variants_distance   = 110000
    wide_format_output           = false
    binder_only                  = false

    // References
    genome_reference = 'grch37'

    // Options: Predictions
    tools = 'mhcnuggets'

    // Options: Filter variants by user-defined proteome
    proteome_reference = null

    // External tools
    external_tools_meta = "${projectDir}/assets/external_tools_meta.json"
    netmhc_system       = 'linux'
    netmhcpan_path      = null
    netmhciipan_path    = null

    // Options: Peptides
    min_peptide_length_classI  = 8
    max_peptide_length_classI  = 12
    min_peptide_length_classII = 8
    max_peptide_length_classII = 25

    // Options: Annotation
    wild_type = true

    // Options: Output
    fasta_output = false
    fasta_peptide_flanking_region_size = 25

    // MultiQC options
    multiqc_config              = null
    multiqc_title               = null
    multiqc_logo                = "$projectDir/assets/nf-core-epitopeprediction_logo_light.png"
    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'
        // TODO https://github.com/nf-core/modules/issues/6694
        // For now if you're using arm64 you have to use wave for the sake of the maintainers
        // wave profile
        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_grch38             { includeConfig 'conf/test_grch38.config' }
    test_peptides           { includeConfig 'conf/test_peptides.config' }
    test_proteins           { includeConfig 'conf/test_proteins.config' }
    test_mhcnuggets         { includeConfig 'conf/test_mhcnuggets.config' }
    test_mhcflurry          { includeConfig 'conf/test_mhcflurry.config' }
    test_netmhcpan          { includeConfig 'conf/test_netmhcpan.config' }
    test_netmhciipan        { includeConfig 'conf/test_netmhciipan.config' }
    test_wide_format_output { includeConfig 'conf/test_wide_format_output.config' }
    test_full               { includeConfig 'conf/test_full.config' }
    test_fasta_output       { includeConfig 'conf/test_fasta_output.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/epitopeprediction 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"


// 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'

// 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"
}

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

manifest {
    name            = 'nf-core/epitopeprediction'
    contributors    = [
        [
            name: 'Christopher Mohr',
            affiliation: 'Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany',
            email: '',
            github: '@christopher-mohr',
            contribution: ['author','maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Jonas Scheid',
            affiliation: 'Department of Peptide-based Immunotherapy, Institute of Immunology, University of Tübingen and University Hospital Tübingen and Quantitative Biology Center (QBIC), University of Tübingen',
            email: 'jonas.scheid@uni-tuebingen.de',
            github: '@jonasscheid',
            contribution: ['author','maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0002-5923-1343'
        ],
        [
            name: 'Alexander Peltzer',
            affiliation: 'Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany',
            email: '',
            github: '@apeltzer',
            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: 'Marissa Dubbelaar',
            affiliation: 'Department of Peptide-based Immunotherapy, Institute of Immunology, University of Tübingen and University Hospital Tübingen and Quantitative Biology Center (QBIC), University of Tübingen',
            email: '',
            github: '@marissaDubbelaar',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: 'Gisela Gabernet',
            affiliation: 'Quantitative Biology Center (QBIC), University of Tübingen',
            email: '',
            github: '@ggabernet',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: 'Sabrina Krakau',
            affiliation: 'Quantitative Biology Center (QBIC), University of Tübingen',
            email: '',
            github: '@skrakau',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: 'Leon Kuchenbecker',
            affiliation: 'Kohlbacher Lab',
            email: '',
            github: '@lkuchenb',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: 'Alina Bauer',
            affiliation: '',
            email: '',
            github: '@alina-bauer',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: 'Axel Walter',
            affiliation: 'Department of Peptide-based Immunotherapy, Institute of Immunology, University of Tübingen and University Hospital Tübingen and Quantitative Biology Center (QBIC), University of Tübingen',
            email: 'axel.walter@uni-tuebingen.de',
            github: '@axelwalter',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0003-2442-7538'
        ]
    ]
    homePage        = 'https://github.com/nf-core/epitopeprediction'
    description     = """A fully reproducible and state of the art epitope prediction pipeline."""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=25.04.0'
    version         = '3.1.1'
    doi             = ''
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
    id 'nf-co2footprint@1.0.0' // Trace and report energy consumption in CO2-equivalents
}

co2footprint {
    // Reuse the timestamp of the other reports, a variable declaration here is rejected by the strict config parser
    traceFile   = "${params.outdir}/pipeline_info/co2footprint_trace_${params.trace_report_suffix}.txt"
    summaryFile = "${params.outdir}/pipeline_info/co2footprint_summary_${params.trace_report_suffix}.txt"
    reportFile  = "${params.outdir}/pipeline_info/co2footprint_report_${params.trace_report_suffix}.html"
}

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

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