nextflow.config

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

// Global default params, used in configs
params {

    // Input options
    input                               = null

    // References
    genome                              = null
    genome_fasta                        = null
    transcript_fasta                    = null
    gtf                                 = null
    igenomes_base                       = 's3://ngi-igenomes/igenomes/'
    igenomes_ignore                     = true
    fasta_delimiter                     = ""

    // Fastq Options
    split_amount                        = 0

    // Read Trimming Options
    min_length                          = 1
    min_q_score                         = 10
    skip_trimming                       = false

    // Cell barcode options
    whitelist                           = null
    barcode_format                      = null
    dedup_tool                          = 'umitools'

    // Library strandness option
    stranded                            = null

    // Mapping
    skip_save_minimap2_index            = false
    kmer_size                           = 14

    // Analysis options
    retain_introns                      = true
    quantifier                          = ''

    // Process Skipping options
    skip_qc                             = false
    skip_nanoplot                       = false
    skip_toulligqc                      = false
    skip_fastqc                         = false
    skip_fastq_nanocomp                 = false
    skip_bam_nanocomp                   = false
    skip_rseqc                          = false
    save_genome_secondary_alignment     = false
    save_transcript_secondary_alignment = true
    skip_dedup                          = false
    skip_seurat                         = false
    skip_multiqc                        = false

    // 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/'

    // 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
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.config' }
}

// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

// Load nf-core/scnanoseq custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/scnanoseq.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", "-Ceuo", "pipefail"]

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

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}

manifest {
    name            = 'nf-core/scnanoseq'
    author          = """Austyn Trull, Lara Ianov"""
    homePage        = 'https://github.com/nf-core/scnanoseq'
    description     = """Single-cell/nuclei pipeline for data derived from Oxford Nanopore"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=24.04.2'
    version         = '1.1.0'
    doi             = ''
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

validation {
    defaultIgnoreParams = ["genomes"]
    help {
        enabled = true
        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
        fullParameter = "help_full"
        showHiddenParameter = "show_hidden"
        beforeText = """
-\033[2m----------------------------------------------------\033[0m-
                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
                                        \033[0;32m`._,._,\'\033[0m
\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/${manifest.name}/blob/master/CITATIONS.md
"""
    }
    summary {
        beforeText = validation.help.beforeText
        afterText = validation.help.afterText
    }
}

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