nextflow.config

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

// Global default params, used in configs
params {
  // Workflow flags for SpliZ
  // TODO nf-core: Specify your pipeline's command line flags
  dataname = null
  input_file = null
  SICILIAN = false
  pin_S = 0.01
  pin_z = 0.0
  bounds = 5
  light = false
  svd_type = "normdonor"
  n_perms = 100
  grouping_level_1 = null
  grouping_level_2 = null 
  libraryType = null
  run_analysis = false
  samplesheet = null
  annotator_pickle = null
  exon_pickle = null
  splice_pickle = null 
  meta = null
  gtf = null 
  rank_quant = 0
 
  outdir = './results/${params.dataname}'
  publish_dir_mode = 'copy'

  // Boilerplate options
  genome = false
  genomes = false
  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_name = null
  config_profile_description = false
  config_profile_contact = false
  config_profile_url = false
  validate_params = true
  show_hidden_params = false
  schema_ignore_params = 'genomes'

  // Defaults only, expecting to be overwritten
  max_memory = 800.GB
  max_cpus = 16
  max_time = 240.h

}

// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
process.container = 'kaitlinchaung/spliz:dev'

// 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 {
  sherlock {
    process.executor = 'slurm'
    process.clusterOptions = '-p owners'

    process.memory = { 20.GB * task.attempt }
    process.time = { 1.h * task.attempt }
    process.errorStrategy = { task.exitStatus in [1,130,143,137,104,134,139] ? 'retry' : 'finish' }
    process.maxRetries = 3
  }
  conda {
    docker.enabled = false
    singularity.enabled = false
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = false
    process.conda = "$projectDir/environment.yml"
    createTimeout = "2 h"
  }
  debug { process.beforeScript = 'echo $HOSTNAME' }
  docker {  
    process.container           = 'kaitlinchaung/spliz:v0.8'
    docker.enabled              = true
    docker.userEmulation        = true
    singularity.enabled         = false
    podman.enabled              = false
    shifter.enabled             = false
    charliecloud.enabled        = false
  }
  singularity {
    process.container           = 'kaitlinchaung/spliz:v0.8'
    singularity.enabled         = true
    singularity.autoMounts      = true
    docker.enabled              = false
    podman.enabled              = false
    shifter.enabled             = false
    charliecloud.enabled        = false
  }
  podman {
    singularity.enabled = false
    docker.enabled = false
    podman.enabled = true
    shifter.enabled = false
    charliecloud.enabled = 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' }
  small_test_data   { includeConfig 'small_data/small.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 = 'salzmanlab/spliz'
  author = 'Salzman Lab'
  homePage = 'https://github.com/salzmanlab/SpliZ'
  description = 'Code to calculate the Splicing Z Score (SZS) for single cell RNA-seq splicing analysis'
  mainScript = 'main.nf'
  nextflowVersion = '>=20.04.0'
  version = '1.0dev'
}

// 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
    }
  }
}