nextflow.config

// Global default params, used in configs
params {

  // workflow options
  help = false
  adata = "input.h5ad"
  parameters = "parameters.csv"
  probeset = "probeset.csv"
  probeset_ids = "all"
  markers = "markers.csv"
  run_cs = true
  run_knn = true
  run_rf = true
  run_corr = true
  outdir = './results'

  // Boilerplate options
  name = false
  email = false
  email_on_fail = false
  plaintext_email = false
  monochrome_logs = false
  help = false
  tracedir = "${params.outdir}/pipeline_info"
  awsqueue = false
  awsregion = 'eu-west-1'
  igenomes_ignore = true
  igenomes_base = 's3://ngi-igenomes/igenomes/'
  custom_config_version = 'master'
  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
  hostnames = false
  config_profile_description = false
  config_profile_contact = false
  config_profile_url = false

  // Options: AWSBatch
  clusterOptions = false
  awsqueue = false
  awsregion = 'eu-west-1'

  // Options: Custom config
  config_profile_description = false
  config_profile_contact = false
  config_profile_url = false

  custom_config_version = 'master'
  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
}

// Container slug.
process.container = 'theislab/spapros-pipeline:1.0.0'

// 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 {
  conda { process.conda = "$baseDir/environment.yml" }
  debug { process.beforeScript = 'echo $HOSTNAME' }
  docker {
    docker.enabled = true
    docker.runOptions = '-u \$(id -u):\$(id -g)'
  }
  singularity {
    singularity.enabled = true
    singularity.autoMounts = true
  }
  test { includeConfig 'conf/test.config' }
}

// Load igenomes.config if required
if (!params.igenomes_ignore) {
  includeConfig 'conf/igenomes.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']

timeline {
  enabled = true
  file = "${params.tracedir}/execution_timeline.html"
}
report {
  enabled = true
  file = "${params.tracedir}/execution_report.html"
}
trace {
  enabled = true
  file = "${params.tracedir}/execution_trace.txt"
}
dag {
  enabled = true
  file = "${params.tracedir}/pipeline_dag.svg"
}

manifest {
  name = 'theislab/spapros-pipeline'
  author = 'Louis Kümmerle, Lukas Heumos'
  homePage = 'https://github.com/theislab/spapros-pipeline'
  description = 'Pipeline to select and to evaluate probesets'
  mainScript = 'main.nf'
  nextflowVersion = '>=19.10.0'
  version = '1.0.0'
}

// 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
    }
  }
}