nextflow.config

/*
========================================================================================
    nf-core/circrna Nextflow config file
========================================================================================
*/

// Global default params, used in configs
params {

  // Workflow flags
  outdir = 'results/'
  publish_dir_mode = 'copy'
  hostnames = false
  tracedir = "${params.outdir}/pipeline_info"
  config_profile_name = null

  // Input files
  input = null
  input_type = null
  phenotype = null

  // Workflow analysis, filtering flags
  module = 'circrna_discovery, mirna_prediction, differential_expression'
  tool = 'ciriquant, circexplorer2, find_circ, mapsplice, dcc, circrna_finder, segemehl'
  tool_filter = 2
  bsj_reads = 2
  mfe = -20.00

  // Save intermediates?
  save_reference = true
  save_qc_intermediates = true
  save_quantification_intermediates = true
  save_mirna_predictions = true
  save_rnaseq_intermediates = true

  // Reference files
  // exclude all others here, iGenomes can handle it (or else cmdline overrides it)
  genome = null

  // BBDUK trimming options
  trim_fastq = false
  adapters = "${projectDir}/bin/adapters.fa"
  k = 12
  ktrim = 'r'
  hdist = 1
  trimq = 20
  qtrim = 'r'
  minlen = 30
  save_trimmed = false

  // STAR aligner options
  alignIntronMax = 1000000
  alignIntronMin = 20
  alignMatesGapMax = 1000000
  alignSJDBoverhangMin = 1
  alignSJoverhangMin = 1
  alignSoftClipAtReferenceEnds = 'No'
  alignTranscriptsPerReadNmax = 10000
  chimJunctionOverhangMin = 15
  chimScoreMin = 15
  chimScoreSeparation = 10
  chimSegmentMin = 10
  genomeLoad = 'NoSharedMemory'
  limitSjdbInsertNsj = 1000000
  outFilterMatchNminOverLread = 0.33
  outFilterMismatchNoverLmax = 0.05
  outFilterMultimapNmax = 20
  outFilterMultimapScoreRange = 1
  outFilterScoreMinOverLread = 0.33
  outSJfilterOverhangMin = '15 15 15 15'
  sjdbOverhang = 100
  sjdbScore = 2
  winAnchorMultimapNmax = 999

  // Boilerplate options
  multiqc_config = false
  email = false
  email_on_fail = false
  max_multiqc_email_size = 25.MB
  plaintext_email = false
  monochrome_logs = false
  help = false
  igenomes_base = 's3://ngi-igenomes/igenomes'
  tracedir = "${params.outdir}/pipeline_info"
  igenomes_ignore = false
  custom_config_version = 'master'
  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
  hostnames = false
  config_profile_name = null
  config_profile_description = false
  config_profile_contact = false
  config_profile_url = false
  validate_params = true
  show_hidden_params = false
  schema_ignore_params = 'genomes,input_paths'

  // Defaults only, expecting to be overwritten
  max_memory = 128.GB
  max_cpus = 16
  max_time = 240.h
}

// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
process.container = 'barryd237/circrna:dev'

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

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

profiles {
  conda {
    docker.enabled = false
    singularity.enabled = false
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = false
    process.conda = "$projectDir/environment.yml"
  }
  debug { process.beforeScript = 'echo $HOSTNAME' }
  docker {
    docker.enabled = true
    singularity.enabled = false
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = false
    // Avoid this error:
    //   WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
    // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
    // once this is established and works well, nextflow might implement this behavior as new default.
    docker.runOptions = '-u \$(id -u):\$(id -g)'
  }
  singularity {
    docker.enabled = false
    singularity.enabled = true
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = false
    singularity.autoMounts = true
  }
  podman {
    singularity.enabled = false
    docker.enabled = false
    podman.enabled = true
    shifter.enabled = false
    charliecloud.enabled = false
  }
  shifter {
    singularity.enabled = false
    docker.enabled = false
    podman.enabled = false
    shifter.enabled = true
    charliecloud.enabled = false
  }
  charliecloud {
    singularity.enabled = false
    docker.enabled = false
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = true
  }
  test { includeConfig 'conf/test.config' }
  test_full { includeConfig 'conf/test_full.config' }
  nuig { includeConfig 'conf/nuig.config' }
}

// 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
env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
}

manifest {
    name            = 'nf-core/circrna'
    author          = 'Barry Digby'
    homePage        = 'https://github.com/nf-core/circrna'
    description     = 'circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.04.0'
    version         = 'dev'
}

// 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
        }
    }
}