nextflow.config

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

// Global default params, used in configs
params {
    // Input options
    input                        = null // sample sheet
    tools                        = null // List of annotation tools to run - snpeff or vep or merge

    // References
    genome                       = 'GRCh38'
    igenomes_base                = 's3://ngi-igenomes/igenomes/'
    snpeff_cache                 = 's3://annotation-cache/snpeff_cache/'
    vep_cache                    = 's3://annotation-cache/vep_cache/'
    igenomes_ignore              = false
    save_reference               = false
    feature_type                 = 'exon'

    // Sequence read information
    save_merged_fastq            = false
    read_length                  = 150 // Required for STAR to build index and align reads

    // Alignment
    aligner                      = 'star'     // Only STAR is currently supported.
    star_twopass                 = true
    star_ignore_sjdbgtf          = false      // Ignore GTF file while creating index or alignment by STAR
    star_max_memory_bamsort      = 0          // STAR parameter limitBAMsortRAM to specify maximum RAM for sorting BAM
    star_bins_bamsort            = 50         // STAR parameter outBAMsortingBinsN to specify number of bins for sorting BAM
    star_max_collapsed_junc      = 1000000    // STAR parameter limitOutSJcollapsed to specify max number of collapsed junctions
    star_max_intron_size         = null       // STAR parameter alignIntronMax to specify the max intron size
    seq_center                   = null
    seq_platform                 = 'illumina' // Required for preparing for BAM headers for GATK to work
    bam_csi_index                = false
    save_unaligned               = false
    save_align_intermeds         = false

    // Preprocessing of alignment
    remove_duplicates            = false
    extract_umi                  = false
    umitools_extract_method      = 'string'
    umitools_bc_pattern          = null
    umitools_bc_pattern2         = null
    umitools_umi_separator       = null

    // Variant calling
    no_intervals                 = false

    // Variant annotation
    bcftools_annotations         = null  // No extra annotation file
    bcftools_annotations_tbi     = null  // No extra annotation file index
    bcftools_columns             = null  // Use all columns from annotation file
    bcftools_header_lines        = null  // No header lines to be added to the VCF file
    download_cache               = false // Do not download annotation cache
    dbnsfp                       = null  // No dbnsfp processed file
    dbnsfp_consequence           = null  // No default consequence for dbnsfp plugin
    dbnsfp_fields                = "rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF" // Default fields for dbnsfp plugin
    dbnsfp_tbi                   = null  // No dbnsfp processed file index
    outdir_cache                 = null  // No default outdir cache
    spliceai_indel               = null  // No spliceai_indel file
    spliceai_indel_tbi           = null  // No spliceai_indel file index
    spliceai_snv                 = null  // No spliceai_snv file
    spliceai_snv_tbi             = null  // No spliceai_snv file index
    vep_custom_args              = "--everything --filter_common --per_gene --total_length --offline --format vcf" // Default arguments for VEP
    vep_dbnsfp                   = null  // dbnsfp plugin disabled within VEP
    vep_include_fasta            = false // Don't use fasta file for annotation with VEP
    vep_loftee                   = null  // loftee plugin disabled within VEP
    vep_out_format               = "vcf"
    vep_spliceai                 = null  // spliceai plugin disabled within VEP
    vep_spliceregion             = null  // spliceregion plugin disabled within VEP

    // Skip steps
    skip_baserecalibration       = false
    skip_exon_bed_check          = false
    skip_intervallisttools       = false
    skip_multiqc                 = false
    skip_variantannotation       = false
    skip_variantfiltration       = false

    // GATK intervallist parameters
    gatk_interval_scatter_count  = 25

    // GATK haplotypecaller parameters
    gatk_hc_call_conf            = 20
    generate_gvcf                = false

    //GATK variant filter parameters
    gatk_vf_window_size          = 35
    gatk_vf_cluster_size         = 3
    gatk_vf_fs_filter            = 30.0
    gatk_vf_qd_filter            = 2.0

    // 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                     = System.getenv('HOOK_URL')
    help                         = false
    help_full                    = false
    show_hidden                  = false
    version                      = false
    modules_testdata_base_path   = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/data/'
    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
}

// workflow output
outputDir = params.outdir
workflow.output.mode = params.publish_dir_mode

// 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 nf-core/rnavar 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/rnavar 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/rnavar.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/rnavar'
    contributors    = [
        [
            name: 'Praveen Raj',
            affiliation: 'Barntumörbanken - Karolinska Institutet',
            github: '@praveenraj2018',
            contribution: ['author'],
        ],
        [
            name: 'Maxime U Garcia',
            affiliation: 'National Genomics Infrastructure',
            email: 'maxime.garcia@scilifelab.se',
            github: '@maxulysse',
            contribution: ['author', 'maintainer'],
            orcid: '0000-0003-2827-9261',
        ],
        [
            name: 'Nicolas Vannieuwkerke',
            affiliation: 'CMGG',
            email: 'nicolas.vannieuwkerke@ugent.be',
            github: '@nvnieuwk',
            contribution: ['maintainer'],
            orcid: '0009-0003-5619-1555',
        ],
        [
            name: ' Friederike Hanssen',
            affiliation: 'Seqera',
            github: '@friederikehanssen',
            contribution: ['contributor'],
            orcid: '0009-0001-9875-5262',
        ],
    ]
    homePage        = 'https://github.com/nf-core/rnavar'
    description     = """GATK4 RNA variant calling pipeline"""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=25.10.2'
    version         = '1.2.3'
    doi             = '10.5281/zenodo.6669636'
}

// Nextflow plugins
plugins {
    id 'nf-core-utils@0.4.0' // nf-core-utils is a collection of utilities for Nextflow pipelines
    id 'nf-schema@2.6.1'     // 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'
includeConfig 'conf/modules/annotate.config'
includeConfig 'conf/modules/prepare_cache.config'