nextflow.config

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

// Global default params, used in configs
params {

  //MS params
  input = null
  irts = null
  input_sheet_dda = null
  generate_spectral_library = false
  merge_libraries = false
  align_libraries = false
  min_overlap_for_merging = 100
  generate_pseudo_irts = false
  irts_from_outer_quantiles = false
  n_irts = 250
  library_rt_fdr = 0.01
  unimod = "https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/unimod.xml"

  skip_dia_processing = false
  skip_decoy_generation = false
  run_msstats = true
  mztab_export = false
  generate_plots = true

  irt_min_rsq = 0.95
  irt_alignment_method = 'lowess'
  irt_n_bins = 10
  irt_min_bins_covered = 8
  min_transitions = 6
  max_transitions = 6
  mz_extraction_window_ms1 = 10
  mz_extraction_window_ms1_unit = 'ppm'
  mz_extraction_window = 30
  mz_extraction_window_unit = 'ppm'
  rt_extraction_window = 600
  use_ms1 = true
  min_upper_edge_dist = 0.0

  // Pyprophet default parameters are taken from https://github.com/PyProphet/pyprophet
  pyprophet_classifier = 'LDA'
  pyprophet_fdr_ms_level = 'ms1ms2'
  pyprophet_global_fdr_level = 'protein'
  pyprophet_peakgroup_fdr = 0.01
  pyprophet_peptide_fdr = 0.01
  pyprophet_protein_fdr = 0.01
  pyprophet_pi0_start = 0.1
  pyprophet_pi0_end = 0.5
  pyprophet_pi0_steps = 0.05

  // DIAlignR default parameters are taken from https://github.com/Roestlab/DIAlignR
  dialignr_global_align_fdr = 0.01
  dialignr_analyte_fdr = 0.01
  dialignr_unalign_fdr = 0.01
  dialignr_align_fdr = 0.05
  dialignr_query_fdr = 0.05
  dialignr_xicfilter = "sgolay"
  dialignr_parallelization = true

  decoy_method = 'shuffle'

  force_option = false
  cache_option = 'normal'

  // Workflow flags
  outdir = './results'
  publish_dir_mode = 'copy'

  // Boilerplate options
  email = false
  email_on_fail = false
  plaintext_email = false
  monochrome_logs = false
  help = false
  tracedir = "${params.outdir}/pipeline_info"
  custom_config_version = 'master'
  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
  hostnames = false
  config_profile_name = false
  config_profile_description = false
  config_profile_contact = false
  config_profile_url = false
  validate_params = true
  show_hidden_params = false
  schema_ignore_params = 'input_paths'

  // 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/diaproteomics:1.2.4'

// 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
    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_skip_processing { includeConfig 'conf/test_skip_processing.config'}
  test_no_merge { includeConfig 'conf/test_no_merge.config'}
  test_no_align { includeConfig 'conf/test_no_align.config'}
  test_with_library { includeConfig 'conf/test_with_library.config'}
  test_with_library_with_decoys { includeConfig 'conf/test_with_library_with_decoys.config'}
  test_without_library_with_irts { includeConfig 'conf/test_without_library_with_irts.config' }
  test_with_library_without_irts { includeConfig 'conf/test_with_library_without_irts.config' }
  test_full { includeConfig 'conf/test_full.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/diaproteomics'
  author = 'Leon Bichmann'
  homePage = 'https://github.com/nf-core/diaproteomics'
  description = 'Automated quantitative analysis of DIA proteomics mass spectrometry measurements.'
  mainScript = 'main.nf'
  nextflowVersion = '>=20.04.0'
  version = '1.2.4'
}

// 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
    }
  }
}