nextflow.config

/*
 * -------------------------------------------------
 *  nf-core/rvfvtyping Nextflow config file
 * -------------------------------------------------
 * Default config options for all environments.
 */

// Global default params, used in configs
params {

  // Input options
  input                        = null
  segment                      = ''

  // Diamond options
  skip_diamond                 = false    
  db                           = "$projectDir/db/viral.protein.faa.dmnd.gz"          
  


  // Boilerplate options
  outdir                       = './results'
  publish_dir_mode             = 'copy'
  enable_conda                 = false
  multiqc_config               = false
  email                        = false
  email_on_fail                = false
  max_multiqc_email_size       = 25.MB
  plaintext_email              = false
  monochrome_logs              = false
  help                         = false
  tracedir                     = "${params.outdir}/pipeline_info"

  // config options
  custom_config_version        = 'master'
  custom_config_base           = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
  hostnames                    = [:]
  config_profile_description   = false
  config_profile_contact       = false
  config_profile_url           = false
  validate_params              = true
  show_hidden_params           = false
  schema_ignore_params         = 'modules,work,enable_conda,db'

  // 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              = 'rvfvtyping-env'

// Load base.config by default for all pipelines
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")
//}

profiles {
   debug { process.beforeScript = 'echo $HOSTNAME' }
  conda {
    params.enable_conda         = true
    docker.enabled              = false
    singularity.enabled         = false
    podman.enabled              = false
    shifter.enabled             = false
    charliecloud                = false
    process.conda               = "$projectDir/environment.yml"
  }
  docker {
    process.container           = 'johnjuma/rvfvtyping:latest'
    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                = 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' }
}
// Increase time available to build Conda environment
conda { createTimeout = "120 min" }

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


// 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            = 'rvfvtyping'
  author          = '@ajodeh-juma'
  homePage        = 'https://github.com/ajodeh-juma/rvfvtyping'
  description     = 'Identify Rift Valley Fever virus lineages of a nucleotide sequence'
  mainScript      = 'main.nf'
  nextflowVersion = '>=20.04.0'
  version         = '1.0'
}

// 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
    }
  }
}