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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/quantms Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Workflow flags
input = null // the sdrf and spectra parameters are inferred from this one
root_folder = null
local_input_type = 'mzML'
database = null
acquisition_method = null
// Tools flags
posterior_probabilities = 'percolator'
add_decoys = false
enable_pmultiqc = true
search_engines = 'comet'
run_fdr_cutoff = 0.10
protein_level_fdr_cutoff = 0.01
psm_level_fdr_cutoff = 0.01
// Debug level
decoydatabase_debug = 0
pp_debug = 0
idfilter_debug = 0
idscoreswitcher_debug = 0
iso_debug = 0
db_debug = 0
idpep_debug = 0
percolator_debug = 0
consensusid_debug = 0
idmapper_debug = 0
luciphor_debug = 0
protein_inference_debug = 0
plfq_debug = 0
// decoys
decoy_string = 'DECOY_'
decoy_string_position = 'prefix'
decoy_method = 'reverse'
shuffle_max_attempts = 30
shuffle_sequence_identity_threshold = 0.5
// peak picking if used
openms_peakpicking = false
peakpicking_inmemory = false
peakpicking_ms_levels = null // means all/auto
//Isobaric analyze
labelling_type = null
reference_channel = 126
min_precursor_intensity = 1.0
reporter_mass_shift = 0.002
select_activation = 'HCD'
isotope_correction = true
iso_normalization = false
min_reporter_intensity = 0.0
min_precursor_purity = 0.0
precursor_isotope_deviation = 10.0
// shared search engine parameters
enzyme = 'Trypsin'
num_enzyme_termini = 'fully'
allowed_missed_cleavages = 2
precursor_mass_tolerance = 5
precursor_mass_tolerance_unit = 'ppm'
fixed_mods = 'Carbamidomethyl (C)'
variable_mods = 'Oxidation (M)'
enable_mod_localization = false
mod_localization = 'Phospho (S),Phospho (T),Phospho (Y)'
fragment_mass_tolerance = 0.03
fragment_mass_tolerance_unit = 'Da'
fragment_method = 'HCD' //currently unused. hard to find a good logic to beat the defaults
isotope_error_range = '0,1'
instrument = null //auto-determined from tolerances
protocol = 'automatic'
min_precursor_charge = 2
max_precursor_charge = 4
min_peptide_length = 6
max_peptide_length = 40
num_hits = 1
max_mods = 3
min_pr_mz = null
max_pr_mz = null
min_fr_mz = null
max_fr_mz = null
// PeptideIndexer flags
IL_equivalent = true
unmatched_action = "warn"
// IDPEP flags
outlier_handling = "none"
// Percolator flags
train_FDR = 0.05
test_FDR = 0.05
FDR_level = 'peptide-level-fdrs'
klammer = false
description_correct_features = 0
subset_max_train = 300000
// ConsensusID
consensusid_algorithm = 'best'
min_consensus_support = 1
consensusid_considered_top_hits = 0
// Luciphor options
luciphor_neutral_losses = null
luciphor_decoy_mass = null
luciphor_decoy_neutral_losses = null
// Epifany
top_PSMs = 1
update_PSM_probabilities = false
// Protein inference
picked_fdr = true
protein_score = 'best' // Other options are "Best", "Product", "Sum"
min_peptides_per_protein = 1
use_shared_peptides = true
// ProteinQuantifier
top = 3
average = 'median'
best_charge_and_fraction = false
normalize = false
ratios = false
fix_peptides = false
include_all = true
export_mztab = true
// ProteomicsLFQ flags
protein_inference_method = 'aggregation'
protein_quant = 'unique_peptides'
quantification_method = 'feature_intensity'
targeted_only = true
mass_recalibration = false
transfer_ids = 'false'
alignment_order = 'star'
add_triqler_output = false
quantify_decoys = false
// DIA-NN
diann_debug = 3
scan_window = 8
scan_window_automatic = true
min_corr = 2.0
corr_diff = 1.0
time_corr_only = true
mass_acc_automatic = true
pg_level = 2
species_genes = false
diann_normalize = true
// MSstats general options
msstats_remove_one_feat_prot = true
ref_condition = null
contrasts = 'pairwise'
skip_post_msstats = false
// MSstats LFQ options
msstatslfq_removeFewMeasurements = true
msstatslfq_feature_subset_protein = 'top3'
msstatslfq_quant_summary_method = 'TMP'
// MSstats ISO options
msstatsiso_useunique_peptide = true
msstatsiso_rmpsm_withfewmea_withinrun = true
msstatsiso_summaryformultiple_psm = 'sum'
msstatsiso_summarization_method = 'msstats'
msstatsiso_global_norm = true
msstatsiso_remove_norm_channel = true
msstatsiso_reference_normalization = true
// PTXQC
enable_qc = false
ptxqc_report_layout = null
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
skip_table_plots = false
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
tracedir = "${params.outdir}/pipeline_info"
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'modules'
enable_conda = false
singularity_pull_docker_container = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = [:]
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
}
// 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' }
ebicluster{
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
conda.createTimeout = '1 h'
conda.useMamba = true
process.executor = 'lsf'
}
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.useMamba = true
}
mamba {
params.enable_conda = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
test { includeConfig 'conf/test_lfq.config' }
test_localize { includeConfig 'conf/test_localize.config' }
test_tmt { includeConfig 'conf/test_tmt.config' }
test_lfq { includeConfig 'conf/test_lfq.config' }
test_dia { includeConfig 'conf/test_dia.config' }
test_full_lfq { includeConfig 'conf/test_full_lfq.config' }
test_full_tmt { includeConfig 'conf/test_full_tmt.config' }
test_full_dia { includeConfig 'conf/test_full_dia.config' }
test_full { includeConfig 'conf/test_full_lfq.config' }
mambaci { includeConfig 'conf/mambaci.config' }
}
// Load module config after profile, so they can depend on overwritten input parameters specific for each profile.
// 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
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// 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_${trace_timestamp}.html"
}
manifest {
name = 'nf-core/quantms'
author = 'Yasset Perez-Riverol'
homePage = 'https://github.com/nf-core/quantms'
description = 'Quantitative Mass Spectrometry nf-core workflow'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
version = '1.1dev'
doi = ''
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}