nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    number-25/LongTranscriptomics Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
//Plugins
plugins {
  id 'nf-schema@2.5.1'
}

// Global default params, used in configs
params {
    // Input options
    input                           = 'assets/samplesheet.csv'
    sequencing_type                 = "ont-drna" // sequencing library [ont-drna OR ont-cdna]
    bam_input                       = false // input premapped bam files. default: [false]
    // References
    genome_fasta                    = null //'data/hg38.analysisSet.fa.gz'
    genome_fasta_index              = null //'data/hg38.analysisSet.fa.fai'
    genome_fasta_sizes              = null
    //custom_genome                 = false // only when providing novel genomes
    skip_prepare_reference          = false // even if paths are hardcoded, files need to be unzipped and so on
    genome_minimap2_index           = null
    transcriptome_fasta             = null // e.g. 'data/gencode.v46.transcripts.fa.gz'
    transcriptome_fasta_index       = null
    transcriptome_minimap2_index    = null
    annotation_gtf                  = null // e.g. 'data/Homo_sapiens.GRCh38.112.gtf.gz'

    //igenomes
    //igenomes_base                   = 's3://ngi-igenomes/igenomes/'
    //igenomes_ignore                 = true

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

    // QC
    skip_qc                         = false
    skip_bam_qc                     = false
    skip_alfred                     = false
    skip_samtools_flagstat          = false
    //alfred_options
    //extra_alfred_options          = null
    skip_nanoq                      = false
    //extra_nanoq_options
    skip_sequali                    = false
    //extra_sequali_options
    skip_cramino                    = false
    cramino_min_length              = 0 // minimum read length to consider [default: 0]
    //extra_cramino_options
    skip_samtools_flagstat          = false
    skip_ngs_bits                   = false
    ngs_bits_skip_contamination     = false // default: [false]
    ngs_bits_build                  = 'hg38' // options: [hg38, hg19, non_human]
    //extra_ngs_bits_options          = null

    // MAPPING
    transcriptome_mapping           = true
    // minimap2 options
    skip_mapping                    = false
    //extra_minimap2_options          = null

    // BAM to BIGWIG
    skip_bam_to_bigwig              = false

    // TRANSCRIPT RECONSTRUCTION
    // FLAIR
    skip_flair                      = false
    skip_flair_correct              = false
    extra_flair_correct_options     = null
    skip_flair_collapse             = false
    extra_flair_collapse_options    = null
    // BAMBU
    skip_bambu                      = true
    extra_bambu_options             = null
    // STRINGTIE2
    skip_stringtie                  = false
    extra_stringtie_options         = null
    // ISOQUANT
    skip_isoquant                   = true
    skip_isoquant_correction        = false
    extra_isoquant_options          = null
    // TALON may be added eventually

    // TRANSCRIPTOME QC
    skip_jaccard                    = false
    skip_gffcompare                 = false
    extra_gffcompare_options        = null
    // SQANTI
    skip_sqanti_all                 = false
    skip_sqanti_qc                  = false
    sqanti_qc_reference             = 'human'
    sqanti_qc_cage                  = true
    sqanti_qc_cage_path             = null // path to cage data
    sqanti_qc_polyA_sites           = true
    sqanti_qc_polyA_sites_path      = null // path to polyA sites data
    sqanti_qc_polyA_motif           = true
    sqanti_qc_polyA_motif_path      = null // path to polyA motif data
    sqanti_qc_intron_junctions      = true
    sqanti_qc_intron_path           = null // path to intron junction data
    extra_sqanti_qc_options         = null
    // skip_sqanti_filter           = false
    // extra_sqanti_filter_options  = null
    // skip_sqanti_recover          = false
    // extra_sqanti_recover_options = null

    // FUSION GENE DETECTION
    // JAFFAL
    skip_jaffal                     = true
    skip_jaffal_download            = true
    jaffal_reference                = null

    // TRANSCRIPT QUANTIFICATION
    skip_transcript_quantification  = false
    skip_oarfish                    = false

    // CONTAMINATION / UNMAPPED READ PROFILING
    skip_sylph                      = false
    sylph_database                  = "data/gtdb-r226-c1000-dbv1.syldb"
    sylph_database_name             = "GTDB_r226"

    // Boilerplate options
    outdir                          = null
    publish_dir_mode                = 'copy'
    email                           = null
    plaintext_email                 = false
    monochrome_logs                 = false
    hook_url                        = null
    help                            = 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           = 'dev'
    custom_config_base              = 'conf/base.config'
    config_profile_contact          = 'deancombio@pm.me'
    config_profile_url              = ''

    // Max resource options
    // Defaults only, expecting to be overwritten
    //max_memory                      = '32.GB'
    //max_cpus                        = 10
    //max_time                        = '48.h'
}

validation {
    help {
        enabled     = true
        beforeText  = "Welcome to LongTranscriptomics, I see you are seeking help."
        afterText   = "Farewell, hopefully this was helpful. Please cite the pipeline owners when using this pipeline."
        command     = "nextflow run . -profile <profile> --outdir <outdir>"
    }
}

// Load base.config by default for all pipelines - uncomment this when using custom config for your compute environment
    includeConfig 'conf/base.config'

// Load nf-core custom profiles from different Institutions
//try {
//    includeConfig "${params.custom_config_base}/nfcore_custom.config"
//} catch (Exception e) {
//    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
//}

// Load nf-core 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 number-25/LongTranscriptomics custom profiles from different institutions.
//try {
//    includeConfig "${params.custom_config_base}/pipeline/directrna.config"
//} catch (Exception e) {
//    System.err.println("WARNING: Could not load nf-core/config/directrna profiles: ${params.custom_config_base}/pipeline/directrna.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', 'defaults']
        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' }
}

// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / 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'

// Load igenomes.config if required
//if (!params.igenomes_ignore) {
//includeConfig 'conf/igenomes.config'
//} else {
//    params.genomes = [:]
//}

// 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"
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', '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            = 'number-25/LongTranscriptomics'
    author          = """Dean Bašić"""
    homePage        = 'https://github.com/number-25/LongTranscriptomics'
    description     = """Analysis pipeline for ONT directRNA sequencing data"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=24.10.0'
    version         = '1.0dev'
    doi             = ''
}

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

// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}

// Load DSL2 module specific options
//includeConfig "./subworkflows/local/prepare_genome/nextflow.config"
includeConfig "./workflows/nextflow.config"
//includeConfig "modules/local/nanoq/nanoq/nextflow.config"