nextflow.config

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

// Global default params, used in configs
params {

  aligner = 'alevin'
  // 10x V3 chemistry is compatible with V2
  barcode_whitelist = false
  bustools_correct = true
  chemistry = 'V3'
  fasta = false
  genome = false
  gtf = false
  kallisto_gene_map = false
  kallisto_index = false
  outdir = './results'
  input = null
  input_paths = null
  star_index = false
  txp2gene = false
  type = '10x'
  skip_bustools = false
  save_reference = false
  

  //Genome Defaults
  salmon_index = params.genome ? params.genomes[ params.genome ].salmon_index ?: false : false
  fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
  transcript_fasta = params.genome ? params.genomes[ params.genome ].transcript_fasta ?: false : false
  gtf = params.genome ? params.genomes[ params.genome ].gtf ?: false : false
  txp2gene = params.genome ? params.genomes[ params.genome ].txp2gene ?: false : false

  // Template 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_description = false
  config_profile_contact = false
  config_profile_url = false
  validate_params = true
  show_hidden_params = false
  schema_ignore_params = 'genomes,input_paths'
  publish_dir_mode = 'copy'
  config_profile_name = false


  // 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 = 'nfcore/scrnaseq:1.1.0'

// 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 {
    docker.enabled = false
    singularity.enabled = false
    podman.enabled = false
    shifter.enabled = false
    charliecloud = false
    process.conda = "$projectDir/environment.yml"
  }
  debug { process.beforeScript = 'echo $HOSTNAME' }
  docker {
    docker.enabled = true
    fixOwnership = true
    runOptions = "-u \$(id -u):\$(id -g)"
    singularity.enabled = false
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = false
  }
  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_kallisto { includeConfig 'conf/test_kallisto.config'}
  test_full { includeConfig 'conf/test_full.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 = 'nf-core/scrnaseq'
  author = 'Peter J Bailey, Alexander Peltzer, Olga Botvinnik'
  homePage = 'https://github.com/nf-core/scrnaseq'
  description = 'Pipeline for processing of 10xGenomics single cell rnaseq data'
  mainScript = 'main.nf'
  nextflowVersion = '>=20.10.0'
  version = '1.1.0'
}

// 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
    }
  }
}