nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    plant-food-research-open/genepal Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {

    // Input/output options
    input                               = null
    strict_fasta_id_validation          = true
    protein_evidence                    = null
    eggnogmapper_db_dir                 = null
    eggnogmapper_tax_scope              = 1
    rna_evidence                        = null
    liftoff_annotations                 = null
    orthofinder_annotations             = null
    outdir                              = null
    email                               = null
    tags                                = null

    // Repeat annotation options
    repeat_annotator                    = 'repeatmodeler'
    save_annotated_te_lib               = false
    edta_is_sensitive                   = false
    repeatmasker_save_outputs           = false

    // RNASeq pre-processing options
    fastqc_skip                         = true
    fastp_skip                          = false
    min_trimmed_reads                   = 10000
    fastp_extra_args                    = null
    save_trimmed                        = false
    remove_ribo_rna                     = false
    save_non_ribo_reads                 = false
    ribo_database_manifest              = "${projectDir}/assets/rrna-db-defaults.txt"

    // RNASeq alignment options
    star_max_intron_length              = 16000
    star_align_extra_args               = null
    star_save_outputs                   = false
    save_cat_bam                        = false

    // Annotation options
    braker_extra_args                   = null
    liftoff_coverage                    = 0.9
    liftoff_identity                    = 0.9
    eggnogmapper_evalue                 = 0.00001
    eggnogmapper_pident                 = 35

    // Post-annotation filtering options
    allow_isoforms                      = true
    enforce_full_intron_support         = true
    filter_liftoff_by_hints             = true
    eggnogmapper_purge_nohits           = false
    filter_genes_by_aa_length           = 24

    // Annotation output options
    braker_save_outputs                 = false
    add_attrs_to_proteins_cds_fastas    = false
    append_genome_prefix_to_feature_ids = true

    // Evaluation options
    busco_skip                          = false
    busco_lineage_datasets              = 'eukaryota_odb10'

    // Boilerplate options
    publish_dir_mode                    = 'copy'
    email_on_fail                       = null
    plaintext_email                     = false
    monochrome_logs                     = false
    hook_url                            = System.getenv('HOOK_URL')
    max_multiqc_email_size              = '25.MB'
    version                             = false
    help                                = false
    help_full                           = false
    show_hidden                         = 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

}

// Max resources
process {
    resourceLimits = [
        cpus: 16,
        memory: '72.GB',
        time: '7.day'
    ]
}

// 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_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 plant-food-research-open/genepal 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 plant-food-research-open/genepal 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 params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/genepal.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"
}

manifest {
    name            = 'plant-food-research-open/genepal'
    homePage        = 'https://github.com/plant-food-research-open/genepal'
    description     = """A Nextflow pipeline for consensus, phased and pan-genome annotation."""
    mainScript      = 'main.nf'
    defaultBranch   = 'main'
    nextflowVersion = '!>=25.04.0'
    version         = '1.0.1'
    doi             = 'https://doi.org/10.5281/zenodo.14195006'

    author          = """Usman Rashid, Jason Shiller"""
    contributors    = [
        [
            name: 'Usman Rashid',
            affiliation: 'The New Zealand Institute for Plant and Food Research Limited',
            email: 'Usman.Rashid@plantandfood.co.nz',
            github: 'GallVp',
            contribution: [ 'author', 'maintainer', 'contributor' ],
            orcid: '0000-0002-1109-5493'
        ],
        [
            name: ' Jason Shiller',
            affiliation: 'The New Zealand Institute for Plant and Food Research Limited',
            email: 'Jason.Shiller@plantandfood.co.nz',
            github: 'jasonshiller',
            contribution: [ 'author', 'maintainer', 'contributor' ],
            orcid: '0000-0002-7638-4923'
        ]
    ]
}

// 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
    help {
        enabled = true
        command = "nextflow run plant-food-research-open/genepal -revision <version> -profile <docker/singularity/.../institute> --input assemblysheet.csv --protein_evidence proteins.faa --outdir <OUTDIR>"
        fullParameter = "help_full"
        showHiddenParameter = "show_hidden"
    }
}

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