nextflow.config

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

// Global default params, used in configs
params {

    // Input options
    input                      = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv'
    references_only            = false
    cosmic_username            = null
    cosmic_passwd              = null
    qiagen                     = false
    outdir                     = null

    // MultiQC options
    multiqc_config             = null
    multiqc_title              = null
    multiqc_logo               = null
    max_multiqc_email_size     = '25.MB'
    multiqc_methods_description = null

    // Genome
    genome                     = 'GRCh38'
    genomes_base               = "s3://nf-core-awsmegatests/rnafusion/references"
    genomes_ignore             = false
    genome_gencode_version     = 46
    read_length                = 100
    genomes                    = [:]
    fusion_annot_lib           = "https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases/download/v0.3.0/fusion_lib.Mar2021.dat.gz" // path to  dat.gz CTAT genome lib // TODO: Update to latest with s3 link when available

    // Filtering
    tools_cutoff               = 1

    // Trimming
    trim_tail                  = 0
    trim_tail_fusioncatcher    = 0
    adapter_fasta              = []
    save_trimmed_fail          = false
    save_merged                = false
    min_trimmed_reads          = 1

    // Compression
    cram                       = false

    // Alignment options
    star_ignore_sjdbgtf                  = false
    star_limit_bam_sort_ram              = 0
    seq_center                           = ""
    seq_platform                         = ""
    fusioncatcher_limitSjdbInsertNsj     = 2000000
    fusioninspector_limitSjdbInsertNsj   = 1000000

    // Enable tools
    tools                      = null

    // Skip steps
    skip_qc                    = false
    skip_vis                   = false
    skip_vcf                   = false

    // Reference options
    no_cosmic                     = false
    ctatsplicing_cancer_introns   = "https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/CANCER_SPLICING_LIB_SUPPLEMENT/cancer_introns.GRCh38.Jun232020.tsv.gz"
    species                       = "homo_sapiens"
    dfam_version                  = 3.8
    pfam_version                  = 37.4
    dfam_hmm                      = "https://www.dfam.org/releases/Dfam_${params.dfam_version}/infrastructure/dfamscan/${params.species}_dfam.hmm"
    dfam_h3f                      = "https://www.dfam.org/releases/Dfam_${params.dfam_version}/infrastructure/dfamscan/${params.species}_dfam.hmm.h3f"
    dfam_h3i                      = "https://www.dfam.org/releases/Dfam_${params.dfam_version}/infrastructure/dfamscan/${params.species}_dfam.hmm.h3i"
    dfam_h3m                      = "https://www.dfam.org/releases/Dfam_${params.dfam_version}/infrastructure/dfamscan/${params.species}_dfam.hmm.h3m"
    dfam_h3p                      = "https://www.dfam.org/releases/Dfam_${params.dfam_version}/infrastructure/dfamscan/${params.species}_dfam.hmm.h3p"
    pfam_file                     = "http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam${params.pfam_version}/Pfam-A.hmm.gz"
    annot_filter_url              = "https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm"

    // Path to fusion outputs
    arriba_fusions                = null
    starfusion_fusions            = null
    fusioncatcher_fusions         = null
    fusioninspector_fusions       = null
    whitelist                     = null

    // Boilerplate options
    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/'
    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)'
    }
    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'
    }
    test {
        includeConfig 'conf/test.config'
    }
    test_build {
        includeConfig 'conf/test_build.config'
    }
    test_full {
        includeConfig 'conf/test_full.config'
    }

    gitpod {
        executor.name           = 'local'
        executor.cpus           = 4
        executor.memory         = 8.GB
        process {
            resourceLimits = [
                memory: 8.GB,
                cpus  : 4,
                time  : 1.h
            ]
        }
    }
    gpu {
        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
        apptainer.runOptions    = '--nv'
        singularity.runOptions  = '--nv'
    }
}

// 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/rnafusion 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/rnafusion custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/rnafusion.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 genomes.config if required
includeConfig !params.genomes_ignore ? 'conf/genomes.config' : 'conf/genomes_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/rnafusion'
    contributors    = [
        [
            name: 'Martin Proks',
            affiliation: '',
            email: '',
            github: '@matq007',
            contribution: ['author'],
            orcid: ''
        ],
        [
            name: 'Annick Renevey',
            affiliation: 'SciLifeLab, Karolinska Institutet',
            email: 'annick.renevey@scilifelab.se',
            github: '@rannick',
            contribution: ['author', 'maintainer'],
            orcid: '0000-0001-7411-6063'
        ],
        [
            name: 'Maxime U Garcia',
            affiliation: 'Seqera',
            email: 'maxime.garcia@seqera.io',
            github: '@maxulysse',
            contribution: ['author'],
            orcid: '0000-0003-2827-9261'
        ],
        [
            name: 'Anabella Trigila',
            affiliation: 'ZS Associates',
            email: '',
            github: '@atrigila',
            contribution: ['contributor', 'maintainer'],
            orcid: ''
        ],
        [
            name: 'Nicolas Vannieuwkerke',
            affiliation: 'Center for Medical Genetics Ghent',
            email: '',
            github: '@nvnieuwk',
            contribution: ['contributor', 'maintainer'],
            orcid: ''
        ],
        [
            name: 'Delfina Terradas',
            affiliation: 'ZS Associates',
            email: '',
            github: '@delfiterradas',
            contribution: ['contributor'],
            orcid: ''
        ]

    ]
    homePage        = 'https://github.com/nf-core/rnafusion'
    description     = """Nextflow rnafusion analysis pipeline, part of the nf-core community."""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=24.10.5'
    version         = '4.1.0'
    doi             = '10.5281/zenodo.17641566'
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.4.2' // 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 nf-core/rnafusion -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  nf-core/rnafusion ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
        afterText = """${manifest.doi ? "\n* 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/nf-core/rnafusion/blob/master/CITATIONS.md
"""
    }
    summary {
        beforeText = validation.help.beforeText
        afterText = validation.help.afterText
        hideParams = ["cosmic_username", "cosmic_passwd"]
    }
}

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