nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   runthis Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/



// Global default params, used in configs
params {

    inputdir                   = "fastq_files"
    outdir                     = "merged_fastq_files"

    max_memory = '128.GB'
    max_cpus = 8
    max_time = '72.h'


    // Boilerplate options
    tracedir                   = "${params.outdir}/pipeline_info"
    publish_dir_mode           = 'copy'
    email                      = null
    email_on_fail              = null
    plaintext_email            = false
    monochrome_logs            = false
    hook_url                   = null
    help                       = false
    validate_params            = true
    show_hidden_params         = false
    schema_ignore_params       = 'genomes'
    enable_conda               = false


}

process {

  executor="sge"
  penv = "smp"
  clusterOptions = { "-l mem=${task.memory.giga}G" }

  // Defaults for all processes
  cpus = { check_max( 1 * task.attempt, 'cpus' ) }
  memory = { check_max( 7.GB * task.attempt, 'memory' ) }
  time = { check_max( 4.h * task.attempt, 'time' ) }

  errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
  maxRetries = 1
  maxErrors = '-1'

}


// For the clipseq pipeline, set TMPDIR to avoid this: https://github.com/nf-core/clipseq/issues/31
env {
	_JAVA_OPTIONS="-Djava.io.tmpdir=./"
	TMPDIR="./"
}


// 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}.html"
}

manifest {
    name            = 'merge_fastq'
    author          = 'LC'
    homePage        = 'https://github.com/UCL-BLIC/merge_fastq'
    description     = 'Nextflow pipeline that for each sample, combined Fastq files from different lanes into a single R1/R2 FastQ file'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.10.3'
    version         = '2.0'
    doi             = ''
}


// 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
        }
    }
}