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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
id_only = false
// Input options and validation of sdrf files
input = null
validate_ontologies = true // Enable to validate ontology terms in the SDRF
skip_ms_validation = false // Skip the validation of the MS metadata in the SDRF
skip_factor_validation = true // Skip factor values validation, factor values are important for downstream analysis
skip_experimental_design_validation = false // Skip the validation of the experimental design in the SDRF (replicates, etc)
use_ols_cache_only = true // Use only the OLS cache for ontology validation (no network requests)
// Tools flags
posterior_probabilities = 'percolator'
add_decoys = false
skip_rescoring = false
search_engines = 'comet'
sage_processes = 1
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
extractpsmfeature_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
protein_quant_debug = 0
// decoys
decoy_string = 'DECOY_'
decoy_string_position = 'prefix'
decoy_method = 'reverse'
shuffle_max_attempts = 30
shuffle_sequence_identity_threshold = 0.5
// Spectrum pre-processing
//// Peak picking if used
openms_peakpicking = false
peakpicking_inmemory = false
peakpicking_ms_levels = null // means all/auto
//// Conversion
reindex_mzml = true
// Isobaric analyses
labelling_type = null
isotope_correction = false // Disable plex isotope correction
plex_corr_matrix_file = null // Path to the correction matrix file if disable isotope correction is true
reference_channel = '126'
min_precursor_intensity = 1.0
reporter_mass_shift = 0.002
select_activation = 'HCD'
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_peaks = 10 //minimum number of peaks in a spectrum
min_pr_mz = null
max_pr_mz = null
min_fr_mz = null
max_fr_mz = null
// MSRESCORE flags
ms2rescore = false
ms2pip_model_dir = null
rescore_range = 'independent_run'
ms2pip_model = 'HCD2021'
feature_generators = 'deeplc,ms2pip'
calibration_set_size = 0.15
// SNR features flags
add_snr_feature_percolator = false
// PeptideIndexer flags
IL_equivalent = true
unmatched_action = "warn"
// IDPEP flags
outlier_handling = "none"
// DDA_ID flags
export_decoy_psm = true
// Percolator flags
train_FDR = 0.05
test_FDR = 0.05
fdr_level = 'psm_level_fdrs'
klammer = false
description_correct_features = 0
subset_max_train = 300000
// ConsensusID
consensusid_algorithm = 'best'
min_consensus_support = 0
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'
mass_recalibration = false
alignment_order = 'star'
add_triqler_output = false
quantify_decoys = false
// ProteomicsLFQ MBR parameters
targeted_only = true // If false MBR will be applied for quantification of all proteins
feature_with_id_min_score = 0.10
feature_without_id_min_score = 0.75
lfq_intensity_threshold = 1000
// Bruker data
convert_dotd = false
// DIA-NN
diann_version = '1.8.1' // Possible versions are '1.8.1', '1.9.beta.1'
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
diann_speclib = null
// DIA-NN: Extras
skip_preliminary_analysis = false
empirical_assembly_log = null
random_preanalysis = false
random_preanalysis_seed = 42
empirical_assembly_ms_n = 200
// MSstats general options
msstats_remove_one_feat_prot = true
ref_condition = null
contrasts = 'pairwise'
msstats_threshold = 0.05
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
msstats_plot_profile_qc = false
// pmultiqc options
enable_pmultiqc = true
pmultiqc_idxml_skip = true
// 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 = './results'
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
config_profile_contact = null
config_profile_url = null
// Schema validation default options
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.channels = ['conda-forge', 'bioconda']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
conda.createTimeout = '1 h'
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
singularity.pullTimeout = '1 h'
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.enabled = true
wave.freeze = true
wave.strategy = 'conda,container'
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
micromamba {
conda.enabled = true
conda.useMicromamba = true
conda.createTimeout = '1 h'
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
ebicluster {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
conda.createTimeout = '1 h'
conda.useMamba = true
process.executor = 'lsf'
}
test { includeConfig 'conf/test_lfq.config' }
test_localize { includeConfig 'conf/test_localize.config' }
test_tmt { includeConfig 'conf/test_tmt.config' }
test_tmt_corr { includeConfig 'conf/test_tmt_corr.config' }
test_lfq { includeConfig 'conf/test_lfq.config' }
test_lfq_sage { includeConfig 'conf/test_lfq_sage.config' }
test_dia { includeConfig 'conf/test_dia.config' }
test_latest_dia { includeConfig 'conf/test_latest_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' }
test_dda_id { includeConfig 'conf/test_dda_id.config' }
mambaci { includeConfig 'conf/mambaci.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-core/quantms custom profiles from different institutions.
// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/quantms.config" : "/dev/null"
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
charliecloud.registry = 'quay.io'
// 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"
}
// Set bash options
process.shell = """\
bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
"""
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'nf-core/quantms'
author = """Yasset Perez-Riverol"""
homePage = 'https://github.com/bigbio/quantms'
description = """Quantitative Mass Spectrometry nf-core workflow"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.2'
version = '1.3.1dev'
doi = '10.5281/zenodo.7754148'
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
defaultIgnoreParams = ["genomes"]
help {
enabled = true
command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
beforeText = """
-\033[2m----------------------------------------------------\033[0m-
\033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m
\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m
\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m
\033[0;32m`._,._,\'\033[0m
\033[0;35m ${manifest.name} ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/${manifest.name}/blob/master/CITATIONS.md
"""
}
summary {
beforeText = validation.help.beforeText
afterText = validation.help.afterText
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'