nextflow.config

manifest {
  description = 'Synteny analysis' 
  author = 'Chris Wyatt and Simon Murray'
}

// Defaults parameters, expecting to be overwritten
params {
  // Path to input CSV
  input                      = null
  database                   = null
  // Path to results directory
  outdir                     = "results"
  publish_dir_mode           = 'copy'
  // Remove work directories upon pipeline completion
  clean                      = false
  // include basic config
  custom_config              = null
  // Have limiting jobs be optional
  forks                      = null
  // Max resource options
  max_memory                 = '128.GB'
  max_cpus                   =  16
  max_time                   = '48.h'
  // Display help message with nf-validation
  help = null
  //module parameters
  //sra
  ncbi_settings              = null
  certificate                = null
  //cutadapt
  cutadapt_min_overlap       = 3
  cutadapt_max_error_rate    = 0.1
  pacbio                     = false
  iontorrent                 = false
  FW_primer                  = null
  RV_primer                  = null
  single_end                 = false
  //pear
  pear_p_value               = null
  pear_min_overlap           = null
  pear_max_len               = null
  pear_min_len               = null
  pear_trimmed_min_len       = null
  pear_quality               = null
  pear_max_uncalled          = null
  pear_stat_test             = null
  pear_scoring_method        = null
  pear_scoring_method        = null
  pear_phred                 = null
  //vsearch
  fastq_maxee                = null
  fastq_minlen               = null
  fastq_maxns                = null
  fasta_width                = null
  minuniquesize              = 2
  derep_strand               = null
  sintax_cutoff              = null
  sintax_strand              = null
  seed                       = 1312
  //gitpod
  gitpod                     = null
  //defaults used by Eco-Flow when testing, overwrite on command-line with your own resources
  awsqueue                   = 'HUNDRED_QUEUE'
  awsregion                  = 'us-east-1'
  awscli                     = '/home/ec2-user/miniconda/bin/aws'
  s3bucket                   = 's3://nextflow-programmatic/test_env/'
}

plugins {
  id 'nf-co2footprint@1.0.0-beta'
  id 'nf-validation@1.1.3'
  id 'nf-amazon@2.6.0'
}

def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')

co2footprint {
    traceFile   = "${params.outdir}/pipeline_info/co2_emissions/co2footprint_trace_${timestamp}.txt"
    reportFile  = "${params.outdir}/pipeline_info/co2_emissions/co2footprint_report_${timestamp}.html"
    summaryFile  = "${params.outdir}/pipeline_info/co2_emissions/co2footprint_summary_${timestamp}.html"
    ci          = 300
    pue         = 1.4
}

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

// Load custom config if provided
if (params.custom_config != null) {
   try {
       includeConfig "${params.custom_config}"
    } catch (Exception e) {
       System.err.println("WARNING: Could not load config: ${params.custom_config}")
   }
}

// Select a combination of useful profiles i.e. nextflow run -profile local,docker 
profiles {
  local {
    executor.name            = 'local'
  }
  aws_batch {
    includeConfig 'conf/aws_batch.config'
  }
  //Use Docker as the container management software
  docker {
    docker.enabled           = true
    // Remove docker containers after pipeline completes
    docker.remove            = true
    // Sets user for docker to the user who executes pipeline
    docker.runOptions        = '-u $(id -u):$(id -g)'
    // set registry to quay.io
    docker.registry          = "quay.io"
    // Ensure other container engines are unset
    singularity.enabled      = false
    apptainer.enabled        = false
  }
  singularity {
    singularity.enabled      = true
    // Set where singularity cached images are saved
    singularity.cacheDir     = "singularity/cachedir"
    // set registry to quay.io
    singularity.registry     = "quay.io"
    // Ensure other container engines are unset
    docker.enabled           = false
    apptainer.enabled        = false
  }
  apptainer {
    apptainer.enabled        = true
    // Set where singularity cached images are saved
    apptainer.cacheDir       = "apptainer/cachedir"
    // set registry to quay.io
    apptainer.registry       = "quay.io"
    // Ensure other container engines are unset
    docker.enabled           = false
    singularity.enabled      = false
  }
  test_small { includeConfig 'conf/test_small.config' }
  test_full { includeConfig 'conf/test_full.config' }
}

// Load nf-core modules config
includeConfig 'conf/modules.config'

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

// Capturing Nextflow log files into a rsults/pipeline_info directory
timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${timestamp}.html"
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.outdir}/pipeline_info/pipeline_dag_${timestamp}.html"
}

// Ensures work directories and removed when pipeline completes
if (params.clean == true) {
   cleanup = true
}

//Set max forks if parameter provided
if (params.forks) {
   process {
        maxForks = params.forks
   }
}

// 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
        }
    }
}