nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/rnadnavar Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Dbam_laign.configefault config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {

    // Input options - mandatory
    input                           = null  // sample sheet
    input_restart                   = null
    step                            = 'mapping' // Starts with mapping
    skip_tools                      = null       // All tools (markduplicates + baserecalibrator + QC) are used by default
    save_bam_mapped                 = false      // Mapped BAMs not saved
    save_output_as_bam              = false      //Output files from preprocessing are saved as bam and not as cram files
    rna                             = true
    dna                             = true

    // Genome and reference options
    genome                          = 'GRCh38'
    igenomes_base                   = 's3://ngi-igenomes/igenomes/'
    igenomes_ignore                 = false
    save_reference                  = false
    build_only_index                = false // Only build the reference indexes
    download_cache                  = false // Do not download annotation cache
    fasta_fai                       = null
    dict                            = null

    // Sequence read information
    read_length                     = 76 // Required for STAR to build index and align reads TODO: automate
    wes                             = false       // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers

    // Alignment
    bwa                             = null
    bwamem2                         = null
    star_index                      = null
    aligner                         = 'bwa-mem'
    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
    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
    hisat2_build_memory             = "200.GB"
    splicesites                     = null
    remove_duplicates               = false
    save_mapped                     = false      // Mapped BAMs not saved
    hisat2_index                    = null
    dragmap                         = null
    gff                             = null

    // Modify fastqs (trim/split) with FASTP
    trim_fastq          = false // No trimming
    clip_r1             = 0
    clip_r2             = 0
    three_prime_clip_r1 = 0
    three_prime_clip_r2 = 0
    trim_nextseq        = 0
    split_fastq         = 50000000   // FASTQ files will not be split by default by FASTP
    save_trimmed        = false
    save_split_fastqs   = false

    // Variant calling
    defaultvariantcallers           = "sage,strelka,mutect2" // Default variant callers
    no_intervals                    = false
    intervals                       = null
    nucleotides_per_second          = 200000 // Default interval size
    germline_resource               = null
    germline_resource_tbi           = null
    dbsnp                           = null
    dbsnp_tbi                       = null
    known_indels                    = null
    known_indels_tbi                = null
    known_snps                      = null
    known_snps_tbi                  = null
    pon                             = null
    pon_tbi                         = null
    sage_actionablepanel            = null
    sage_highconfidence             = null
    sage_knownhotspots              = null
    sage_custom_args                = "-validation_stringency LENIENT"
    sage_resource_dir               = null
    sage_ensembl_dir                = null
    joint_mutect2                   = false // if true, enables patient-wise multi-sample somatic variant calling

    // GATK intervallist parameters
    gatk_interval_scatter_count     = 25
    ignore_soft_clipped_bases       = true

    // Variant annotation
    tools                     = null  // No default Variant_Calling or Annotation tools
    genesplicer               = null // genesplicer disabled within VEP
    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
    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           = "--no_progress --offline --shift_hgvs 1 --check_existing --tsl --domains --total_length --allele_number --no_escape --xref_refseq --failed 1 --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --format vcf --biotype --force_overwrite --sift p --polyphen p --variant_class --regulatory --allele_number --af_gnomad --af_gnomadg --gene_phenotype --hgvs --hgvsg --max_af"
    vep_cache                 = null // No directory for VEP cache
    vep_include_fasta         = true // Don't use fasta file for annotation with VEP
    vep_dbnsfp                = null
    vep_loftee                = null
    vep_spliceai              = null
    vep_spliceregion          = null
    vep_out_format            = 'vcf'
    vep_cache_version         = 110
    vep_species               = 'homo_sapiens'
    vep_genome                = null
    outdir_cache              = null // No default outdir cache

    //filtering
    whitelist                  = null
    blacklist                  = null
    rnaedits                   = null
    chain                      = null
    rna_pon                    = null
    rna_pon2                   = null
    fasta2                     = null
    refname2                   = null
    refname                    = null

    // 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/rnadnavar/'
    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'
    }
    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'
    }
    // Basic test profile for CI
    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/rnadnavar 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/rnadnavar 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/rnadnavar.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"
}


// 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
    }
}

manifest {
    name            = 'nf-core/rnadnavar'
    contributors    = [
        [
            name: 'Raquel Manzano Garcia',
            affiliation: 'Cancer Research UK',
            email: 'Raquel.ManzanoGarcia@cruk.cam.ac.uk',
            github: '@RaqManzano',
            contribution: ['author', 'maintainer'],
            orcid: '0000-0002-5124-8992'
        ],[
            name: 'Maxime U Garcia',
            affiliation: 'Seqera',
            email: 'maxime.garcia@seqera.io',
            github: '@maxulysse',
            contribution: ['contributor'],
            orcid: '0000-0003-2827-9261'
        ]
        ]
    homePage        = 'https://github.com/nf-core/rnadnavar'
    description     = """Pipeline for RNA and DNA integrated analysis for somatic mutation detection"""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=25.04.0'
    version         = '1.0'
    doi             = ''
}

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules/modules.config'
// prepare reference
includeConfig 'conf/modules/prepare_resources/prepare_cache.config'
includeConfig 'conf/modules/prepare_resources/prepare_genome.config'
includeConfig 'conf/modules/prepare_resources/prepare_intervals.config'
// quality control
includeConfig 'conf/modules/quality_control/quality_control.config'
includeConfig 'conf/modules/quality_control/trimming.config'
// alignment
includeConfig 'conf/modules/alignment/bam_align.config'
includeConfig 'conf/modules/alignment/alignment_to_fastq.config'
// preprocessing
includeConfig 'conf/modules/gatk4_preprocessing/markduplicates.config'
includeConfig 'conf/modules/gatk4_preprocessing/splitncigarreads.config'
includeConfig 'conf/modules/gatk4_preprocessing/prepare_recalibration.config'
includeConfig 'conf/modules/gatk4_preprocessing/recalibrate.config'
// variant calling
includeConfig 'conf/modules/variant_calling/strelka.config'
includeConfig 'conf/modules/variant_calling/mutect2.config'
includeConfig 'conf/modules/variant_calling/sage.config'
// normalization
includeConfig 'conf/modules/normalize/vt.config'
// annotate
includeConfig 'conf/modules/annotate/annotate.config'
// consensus
includeConfig 'conf/modules/consensus/vcf_consensus.config'
// filtering
includeConfig 'conf/modules/filtering/maf_filtering.config'
// prepare second run
includeConfig 'conf/modules/prepare_realignment/filtersamreads.config'
includeConfig 'conf/modules/prepare_realignment/extract_reads_id.config'