nextflow.config

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

// Global default params, used in configs
params {

    // Input options
    input                        = null
    platform                     = null
    protocol                     = null

    // References
    genome                       = null
    primer_set                   = null
    primer_set_version           = null
    primer_fasta                 = null
    primer_left_suffix           = '_LEFT'
    primer_right_suffix          = '_RIGHT'
    save_reference               = false
    additional_annotation        = null

    // Nanopore options
    fastq_dir                    = null
    sequencing_summary           = null
    min_barcode_reads            = 100
    min_guppyplex_reads          = 10
    artic_minion_model_dir       = null
    artic_minion_model           = null
    skip_pycoqc                  = false
    skip_nanoplot                = false

    // Nanopore/Illumina options
    skip_freyja                  = false
    skip_freyja_boot             = false
    freyja_repeats               = 100
    freyja_depthcutoff           = 0
    freyja_db_name               = 'freyja_db'
    freyja_barcodes              = null
    freyja_lineages              = null
    skip_mosdepth                = false
    skip_pangolin                = false
    pango_database               = null
    skip_nextclade               = false
    skip_variants_quast          = false
    skip_snpeff                  = false
    skip_variants_long_table     = 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

    // Illumina QC, read trimming and filtering options
    kraken2_db                   = 's3://ngi-igenomes/test-data/viralrecon/kraken2_human.tar.gz'
    kraken2_db_name              = 'human'
    kraken2_variants_host_filter = false
    kraken2_assembly_host_filter = true
    save_trimmed_fail            = false
    skip_fastqc                  = false
    skip_kraken2                 = false
    skip_fastp                   = false
    skip_cutadapt                = false
    skip_noninternal_primers     = false
    threeprime_adapters          = false

    // Illumina variant calling options
    variant_caller               = null
    consensus_caller             = 'bcftools'
    min_mapped_reads             = 1000
    ivar_trim_noprimer           = false
    ivar_trim_offset             = null
    filter_duplicates            = false
    save_unaligned               = false
    save_mpileup                 = false
    skip_ivar_trim               = false
    skip_markduplicates          = true
    skip_picard_metrics          = false
    skip_consensus_plots         = false
    skip_consensus               = false
    skip_variants                = false

    // Illumina de novo assembly options
    assemblers                   = 'spades'
    spades_mode                  = 'rnaviral'
    spades_hmm                   = null
    blast_db                     = null
    min_contig_length            = 200
    min_perc_contig_aligned      = 0.7
    skip_bandage                 = false
    skip_blast                   = false
    skip_abacas                  = false
    skip_plasmidid               = true
    skip_assembly_quast          = false
    skip_assembly                = false

    // 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/viralrecon'
    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_sispa         { includeConfig 'conf/test_sispa.config'         }
    test_nanopore      { includeConfig 'conf/test_nanopore.config'      }
    test_full          { includeConfig 'conf/test_full.config'          }
    test_full_aws      { includeConfig 'conf/test_full.config'          }
    test_full_illumina { includeConfig 'conf/test_full.config'          }
    test_full_nanopore { includeConfig 'conf/test_full_nanopore.config' }
    test_full_sispa    { includeConfig 'conf/test_full_sispa.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/viralrecon 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/viralrecon 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/viralrecon.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            = 'nf-core/viralrecon'
    contributors    = [
        [
            name: 'Sara Monzón',
            affiliation: 'BU-ISCIII',
            email: 'smonzon@isciii.es',
            github: '@saramonzon',
            contribution: ['author', 'maintainer'],
            orcid: '0000-0002-0740-6324'
        ],
        [
            name: 'Sarai Varona',
            affiliation: 'BU-ISCIII',
            email: 's.varona@isciii.es',
            github: '@svarona',
            contribution: ['author', 'maintainer'],
            orcid: '0000-0002-2245-210X'
        ],
        [
            name: 'Harshil Patel',
            affiliation: 'Seqera',
            github: '@drpatelh',
            contribution: ['author'],
            orcid: '0000-0003-2707-7940'
        ],
        [
            name: 'Aengus Stewart',
            affiliation: 'The Francis Crick Institute, UK',
            github: '@stewarta',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'Alexander Peltzer',
            affiliation: 'Boehringer Ingelheim',
            github: '@apeltzer',
            contribution: ['contributor'],
            orcid: '0000-0002-6503-2180'
        ],
        [
            name: 'Alison Meynert',
            affiliation: 'University of Edinburgh, Scotland',
            github: '@ameynert',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'Anthony Underwood',
            affiliation: 'Broken Strings Biosciences, Cambridge, UK',
            github: '@antunderwood',
            contribution: ['contributor'],
            orcid: '0000-0002-8547-4277'
        ],
        [
            name: 'Anton Korobeynikov',
            affiliation: 'Saint Petersburg State University, Russia',
            github: '@asl',
            contribution: ['contributor'],
            orcid: '0000-0002-2937-9259'
        ],
        [
            name: 'Artem Babaian',
            affiliation: 'University of British Columbia, Canada',
            email: 'a.babaian@utoronto.ca',
            github: '@ababaian',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'CJ Jossart',
            affiliation: 'Wisconsin State Laboratory of Hygiene',
            github: '@cjjossart',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'Dmitry Meleshko',
            affiliation: 'Saint Petersburg State University, Russia',
            github: '@1dayac',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'Edgar Garriga Nogales',
            affiliation: 'Centre for Genomic Regulation',
            github: '@edgano',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'Erik Garrison',
            affiliation: 'UCSC',
            github: '@ekg',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'Erika Kvalem',
            affiliation: 'Institute of Bioinformatics Innsbruck',
            github: '@ErikaKvalem',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'Friederike Hanssen',
            affiliation: 'Seqera',
            github: '@FriederikeHanssen',
            contribution: ['contributor'],
            orcid: '0009-0001-9875-5262'
        ],
        [
            name: 'Gisela Gabernet',
            affiliation: 'Yale University',
            email: 'gisela.gabernet@yale.edu',
            github: '@ggabernet',
            contribution: ['contributor'],
            orcid: '0000-0001-7049-9474'
        ],
        [
            name: 'Hugo Tavares',
            affiliation: 'University of Cambridge',
            github: '@tavareshugo',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'James A. Fellows Yates',
            affiliation: 'Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig',
            email: 'jfy133@gmail.com',
            github: 'jfy133',
            contribution: ['contributor'],
            orcid: '0000-0001-5585-6277'
        ],
        [
            name: 'Joao Curado',
            affiliation: 'Flomics Biotech',
            github: '@jcurado-flomics',
            contribution: ['contributor'],
        ],
        [
            name: 'Joon Klaps',
            affiliation: 'KU Leuven, Rega Institute for Medical Research',
            github: 'Joon-Klaps',
            contribution: ['contributor'],
            orcid: '0000-0002-2507-0430'
        ],
        [
            name: 'Jerome Nicod',
            affiliation: 'The Francis Crick Institute, UK',
            github: '@Jeromics',
            contribution: ['contributor'],
        ],
        [
            name: 'Jose Espinosa-Carrasco',
            affiliation: 'Centre for Genomic Regulation',
            github: 'JoseEspinosa',
            contribution: ['contributor'],
            orcid: '0000-0002-1541-042X'
        ],
        [
            name: 'Katrin Sameith',
            affiliation: 'DRESDEN-concept Genome Center',
            github: '@ktrns',
            contribution: ['contributor'],
        ],
        [
            name: 'Kevin Menden',
            affiliation: 'QBiC, University of Tübingen',
            github: '@KevinMenden',
            contribution: ['contributor'],
        ],
        [
            name: 'Lluc Cabus',
            affiliation: 'Flomics Biotech',
            github: '@lcabus-flomics',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'Marta Pozuelo',
            affiliation: 'Flomics Biotech',
            github: '@mpozuelo-flomics',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'Maxime U Garcia',
            affiliation: 'Seqera',
            github: '@maxulysse',
            contribution: ['contributor'],
            orcid: '0000-0003-2827-9261'
        ],
        [
            name: 'Michael L Heuer',
            affiliation: 'Mammoth Biosciences, Inc., San Francisco, CA',
            github: '@heuermh',
            contribution: ['contributor'],
            orcid: '0000-0002-9052-6000'
        ],
        [
            name: 'Miguel Juliá',
            affiliation: 'IBBTEC',
            github: '@MiguelJulia',
            contribution: ['contributor'],
        ],
        [
            name: 'Phil Ewels',
            affiliation: 'Seqera',
            github: '@ewels',
            contribution: ['contributor'],
           orcid: '0000-0003-4101-2502'
        ],
        [
            name: 'Richard Mitter',
            affiliation: 'The Francis Crick Institute, UK',
            github: '@rjmitter',
            contribution: ['contributor'],
        ],
        [
            name: 'Robert Goldstone',
            affiliation: 'The Francis Crick Institute, UK',
            github: '@rjgoldstone',
            contribution: ['contributor'],
        ],
        [
            name: 'Simon Heumos',
            affiliation: 'Quantitative Biology Center (QBiC) Tübingen, University of Tübingen',
            github: '@subwaystation',
            contribution: ['contributor'],
            orcid: '0000-0003-3326-817X'
        ],
        [
            name: 'Stephen Kelly',
            affiliation: 'Memorial Sloan Kettering Cancer Center, USA',
            github: '@stevekm',
            contribution: ['contributor'],
            orcid: ''
        ],
        [
            name: 'Thanh Le Viet',
            affiliation: 'Quadram Institute, UK',
            github: '@thanhleviet',
            contribution: ['contributor'],
            orcid: ''
        ]
    ]
    homePage        = 'https://github.com/nf-core/viralrecon'
    description     = """Assembly and intrahost/low-frequency variant calling for viral samples"""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=25.04.0'
    version         = '3.0.0'
    doi             = 'https://doi.org/10.5281/zenodo.3901628'
}

// 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 {
        ebabled = true
        fullParameter = "help_full"
        showHiddenParameter = "show_hidden"
    }
}

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