Bigbio/Quantms#
https://docs.quantms.org/
QuantMS inputs#
samplesheetfile – Sample Data Relationship Format (SDRF) defines the massspectrometry input files, example:
source name
biological replicate
modification parameters
fragment mass tolerance
data file
The construction of the SDRF can be done using a script, the lessSDRF online tool or directly using Excel or similar spread sheet tools
Fasta file with protein sequences – defines the search space (for the recorded samples by the masspectrometer)
typically protein sequences from one species whose proteome was analyzed
typically from UNIPROT
raw,.dormzMLspectra files
Examples can be found in the proteomics introduction course, see: https://biosustain.github.io/dsp_course_proteomics_intro/material/quantms_input_files.html
Parameters#
Some parameters are overwritten based on the SDRF settings. SDRF file level parameter settings always have prevalance over the pipeline parameters.
All parameters of quantms 1.6.0 (JSON)
{
"custom_config_base": "https://raw.githubusercontent.com/nf-core/configs/master",
"min_peptide_length": 6,
"alignment_order": "star",
"fdr_level": "psm_level_fdrs",
"msstatslfq_removeFewMeasurements": true,
"plaintext_email": false,
"luciphor_debug": 0,
"isotope_correction": false,
"extractpsmfeature_debug": 0,
"ms2_fragment_method": "HCD",
"msstatsiso_rmpsm_withfewmea_withinrun": true,
"subset_max_train": 300000,
"protein_score": "best",
"feature_with_id_min_score": 0.1,
"ms2rescore": false,
"shuffle_sequence_identity_threshold": 0.5,
"protein_inference_method": "aggregation",
"reindex_mzml": true,
"min_reporter_intensity": 0,
"normalize": false,
"skip_preliminary_analysis": false,
"description_correct_features": 0,
"decoy_string": "DECOY_",
"variable_mods": "Oxidation (M)",
"fragment_mass_tolerance": 0.03,
"msstatslfq_quant_summary_method": "TMP",
"skip_factor_validation": true,
"psm_level_fdr_cutoff": 0.01,
"skip_table_plots": false,
"scan_window_automatic": true,
"enable_diann_mztab": true,
"pmultiqc_idxml_skip": true,
"version": false,
"openms_peakpicking": false,
"publish_dir_mode": "copy",
"input": "az://pxd040621-heweb/PXD040621/mzML/PXD040621.sdrf.tsv",
"feature_without_id_min_score": 0.75,
"msstatsiso_remove_norm_channel": true,
"min_precursor_charge": 2,
"consensusid_algorithm": "best",
"protein_quant": "unique_peptides",
"quant_activation_method": "HCD",
"min_pr_mz": 400,
"max_fr_mz": 1800,
"min_peptides_per_protein": 1,
"precursor_isotope_deviation": 10,
"num_hits": 1,
"precursor_mass_tolerance": 5,
"average": "median",
"decoy_method": "reverse",
"allowed_missed_cleavages": 2,
"max_peptide_length": 40,
"iso_normalization": false,
"protein_level_fdr_cutoff": 0.01,
"random_preanalysis": false,
"diann_debug": 3,
"mass_acc_automatic": true,
"custom_config_version": "master",
"update_PSM_probabilities": false,
"feature_generators": "deeplc,ms2pip",
"msstats_remove_one_feat_prot": true,
"top": 3,
"fixed_mods": "Carbamidomethyl (C)",
"msstatsiso_summaryformultiple_psm": "sum",
"msstats_plot_profile_qc": false,
"root_folder": "az://pxd040621-heweb/PXD040621/mzML",
"pp_debug": 0,
"email": "heweb@dtu.dk",
"fix_peptides": false,
"pg_level": 2,
"use_ols_cache_only": true,
"IL_equivalent": true,
"acquisition_method": "dda",
"empirical_assembly_ms_n": 200,
"peakpicking_inmemory": false,
"run_fdr_cutoff": 0.1,
"lfq_intensity_threshold": 1000,
"protein_inference_debug": 0,
"local_input_type": "mzML",
"quantification_method": "feature_intensity",
"enable_pmultiqc": true,
"outdir": "az://pxd040621-heweb/PXD040621/results-demo-compenv",
"use_shared_peptides": true,
"pipelines_testdata_base_path": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"sage_processes": 1,
"help": false,
"psm_clean": false,
"min_precursor_purity": 0,
"enable_mod_localization": false,
"train_FDR": 0.05,
"skip_ms_validation": false,
"export_mztab": true,
"klammer": false,
"search_engines": "comet,sage",
"force_model": false,
"diann_report_decoys": false,
"idfilter_debug": 0,
"min_fr_mz": 100,
"msstats_threshold": 0.05,
"monochrome_logs": false,
"diann_normalize": true,
"test_FDR": 0.05,
"find_best_model": true,
"precursor_mass_tolerance_unit": "ppm",
"consider_modloss": false,
"protocol": "automatic",
"skip_experimental_design_validation": false,
"diann_export_xic": false,
"add_triqler_output": false,
"targeted_only": true,
"max_multiqc_email_size": "25.MB",
"msstatsiso_useunique_peptide": true,
"min_consensus_support": 0,
"max_precursor_charge": 4,
"validate_params": true,
"consensusid_debug": 0,
"min_peaks": 10,
"isotope_error_range": "0,1",
"best_charge_and_fraction": false,
"met_excision": true,
"mod_localization": "Phospho (S),Phospho (T),Phospho (Y)",
"performance_mode": true,
"num_enzyme_termini": "fully",
"add_decoys": true,
"percolator_debug": 0,
"fragment_mass_tolerance_unit": "Da",
"msstatsiso_summarization_method": "msstats",
"max_pr_mz": 2400,
"trace_report_suffix": "2025-11-26_15-18-48",
"db_debug": 0,
"min_precursor_intensity": 1,
"export_decoy_psm": true,
"species_genes": false,
"picked_fdr": true,
"scan_window": 8,
"iso_debug": 0,
"quick_mass_acc": true,
"msstatsiso_global_norm": true,
"msstatslfq_feature_subset_protein": "top3",
"ms2rescore_fragment_tolerance": 0.05,
"mass_recalibration": false,
"shuffle_max_attempts": 30,
"protein_quant_debug": 0,
"id_only": false,
"database": "az://pxd040621-heweb/PXD040621/mzML/merged_ecoli_with_contaminants.fasta",
"reporter_mass_shift": 0.002,
"rescore_range": "independent_run",
"random_preanalysis_seed": 42,
"calibration_set_size": 0.15,
"quantify_decoys": false,
"reference_channel": "126",
"contrasts": "pairwise",
"idmapper_debug": 0,
"ratios": false,
"enzyme": "Trypsin",
"include_all": true,
"ms2_model": "HCD2021",
"add_snr_feature_percolator": false,
"validate_ontologies": true,
"consensusid_considered_top_hits": 0,
"top_PSMs": 1,
"convert_dotd": false,
"unmatched_action": "warn",
"mzml_features": false,
"skip_rescoring": false,
"msstatsiso_reference_normalization": true,
"idscoreswitcher_debug": 0,
"skip_post_msstats": true,
"decoy_string_position": "prefix",
"max_mods": 3,
"decoydatabase_debug": 0,
"plfq_debug": 0
}
and highlighting the ones that were explicitly set (through the UI, as yaml or json):
{
// definitely change and check
"root_folder": "az://pxd040621-heweb/PXD040621/mzML",
"input": "az://pxd040621-heweb/PXD040621/mzML/PXD040621.sdrf.tsv",
"outdir": "az://pxd040621-heweb/PXD040621/results-demo-compenv",
"database": "az://pxd040621-heweb/PXD040621/mzML/merged_ecoli_with_contaminants.fasta",
"add_decoys": true,
// most likely to double check
"acquisition_method": "dda",
"search_engines": "comet,sage",
"local_input_type": "mzML",
"use_ols_cache_only": true,
"reindex_mzml": true,
"skip_post_msstats": true,
// not changed by let's highlight
"fragment_mass_tolerance": 0.03,
"psm_level_fdr_cutoff": 0.01,
"feature_without_id_min_score": 0.75,
"min_precursor_charge": 2,
"protein_quant": "unique_peptides",
"quant_activation_method": "HCD",
"min_pr_mz": 400,
"max_fr_mz": 1800,
"min_peptides_per_protein": 1,
"precursor_isotope_deviation": 10,
"num_hits": 1,
"precursor_mass_tolerance": 5,
"average": "median",
"decoy_method": "reverse",
"allowed_missed_cleavages": 2,
"max_peptide_length": 40,
"protein_level_fdr_cutoff": 0.01,
"feature_generators": "deeplc,ms2pip",
"fixed_mods": "Carbamidomethyl (C)",
"lfq_intensity_threshold": 1000,
"quantification_method": "feature_intensity",
"use_shared_peptides": true,
"precursor_mass_tolerance_unit": "ppm",
"targeted_only": true,
"min_consensus_support": 0,
"max_precursor_charge": 4,
"min_peaks": 10,
"mod_localization": "Phospho (S),Phospho (T),Phospho (Y)",
"add_decoys": true,
"fragment_mass_tolerance_unit": "Da",
"max_pr_mz": 2400,
"enzyme": "Trypsin",
"include_all": true,
"ms2_model": "HCD2021",
"max_mods": 3
}
Resolved configuration on Seqera#
Seqera give a resolved configuration of the parameters and all settings with respect to the profile setting up the compute environment.
Resolved parameters and profile configuration of a quantms 1.6.0 (JSON) on Azure using the docker profile
params {
root_folder = 'az://pxd040621-heweb/PXD040621/mzML'
local_input_type = 'mzML'
database = 'az://pxd040621-heweb/PXD040621/mzML/merged_ecoli_with_contaminants.fasta'
acquisition_method = 'dda'
id_only = false
input = 'az://pxd040621-heweb/PXD040621/mzML/PXD040621.sdrf.tsv'
validate_ontologies = true
skip_ms_validation = false
skip_factor_validation = true
skip_experimental_design_validation = false
use_ols_cache_only = true
add_decoys = true
skip_rescoring = false
search_engines = 'comet,sage'
sage_processes = 1
run_fdr_cutoff = 0.10
protein_level_fdr_cutoff = 0.01
psm_level_fdr_cutoff = 0.01
psm_clean = false
decoydatabase_debug = 0
pp_debug = 0
extractpsmfeature_debug = 0
idfilter_debug = 0
idscoreswitcher_debug = 0
iso_debug = 0
db_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
decoy_string = 'DECOY_'
decoy_string_position = 'prefix'
decoy_method = 'reverse'
shuffle_max_attempts = 30
shuffle_sequence_identity_threshold = 0.5
openms_peakpicking = false
peakpicking_inmemory = false
peakpicking_ms_levels = null
reindex_mzml = true
mzml_features = false
labelling_type = null
isotope_correction = false
plex_corr_matrix_file = null
reference_channel = '126'
min_precursor_intensity = 1.0
reporter_mass_shift = 0.002
quant_activation_method = 'HCD'
iso_normalization = false
min_reporter_intensity = 0.0
min_precursor_purity = 0.0
precursor_isotope_deviation = 10.0
enzyme = 'Trypsin'
met_excision = true
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'
ms2_fragment_method = 'HCD'
isotope_error_range = '0,1'
instrument = null
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
min_pr_mz = 400
max_pr_mz = 2400
min_fr_mz = 100
max_fr_mz = 1800
ms2rescore = false
ms2_model_dir = null
rescore_range = 'independent_run'
ms2_model = 'HCD2021'
feature_generators = 'deeplc,ms2pip'
calibration_set_size = 0.15
ms2rescore_fragment_tolerance = 0.05
find_best_model = true
force_model = false
consider_modloss = false
add_snr_feature_percolator = false
IL_equivalent = true
unmatched_action = 'warn'
export_decoy_psm = true
train_FDR = 0.05
test_FDR = 0.05
fdr_level = 'psm_level_fdrs'
klammer = false
description_correct_features = 0
subset_max_train = 300000
consensusid_algorithm = 'best'
min_consensus_support = 0
consensusid_considered_top_hits = 0
luciphor_neutral_losses = null
luciphor_decoy_mass = null
luciphor_decoy_neutral_losses = null
top_PSMs = 1
update_PSM_probabilities = false
picked_fdr = true
protein_score = 'best'
min_peptides_per_protein = 1
use_shared_peptides = true
top = 3
average = 'median'
best_charge_and_fraction = false
normalize = false
ratios = false
fix_peptides = false
include_all = true
export_mztab = true
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
targeted_only = true
feature_with_id_min_score = 0.10
feature_without_id_min_score = 0.75
lfq_intensity_threshold = 1000
convert_dotd = false
diann_debug = 3
scan_window = 8
scan_window_automatic = true
performance_mode = true
quick_mass_acc = true
mass_acc_automatic = true
pg_level = 2
species_genes = false
diann_normalize = true
diann_speclib = null
diann_report_decoys = false
diann_export_xic = false
skip_preliminary_analysis = false
empirical_assembly_log = null
random_preanalysis = false
random_preanalysis_seed = 42
empirical_assembly_ms_n = 200
enable_diann_mztab = true
msstats_remove_one_feat_prot = true
ref_condition = null
contrasts = 'pairwise'
msstats_threshold = 0.05
skip_post_msstats = true
msstatslfq_removeFewMeasurements = true
msstatslfq_feature_subset_protein = 'top3'
msstatslfq_quant_summary_method = 'TMP'
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
enable_pmultiqc = true
pmultiqc_idxml_skip = true
multiqc_config = null
multiqc_title = null
multiqc_logo = null
skip_table_plots = false
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
outdir = 'az://pxd040621-heweb/PXD040621/results-demo-compenv'
publish_dir_mode = 'copy'
email = 'heweb@dtu.dk'
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/'
trace_report_suffix = '2025-11-26_15-18-50'
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = 'https://raw.githubusercontent.com/nf-core/configs/master'
config_profile_contact = null
config_profile_url = null
validate_params = true
}
process {
cpus = { 1 * task.attempt }
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }
errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
maxRetries = 1
maxErrors = '-1'
withLabel:process_tiny {
cpus = { 1 }
memory = { 1.GB * task.attempt }
time = { 1.h * task.attempt }
}
withLabel:process_single {
cpus = { 1 }
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }
}
withLabel:process_low {
cpus = { 4 * task.attempt }
memory = { 12.GB * task.attempt }
time = { 6.h * task.attempt }
}
withLabel:process_very_low {
cpus = { 2 * task.attempt}
memory = { 4.GB * task.attempt}
time = { 3.h * task.attempt}
}
withLabel:process_medium {
cpus = { 8 * task.attempt }
memory = { 36.GB * task.attempt }
time = { 8.h * task.attempt }
}
withLabel:process_high {
cpus = { 12 * task.attempt }
memory = { 72.GB * task.attempt }
time = { 16.h * task.attempt }
}
withLabel:process_long {
time = { 20.h * task.attempt }
}
withLabel:process_high_memory {
memory = { 200.GB * task.attempt }
}
withLabel:error_ignore {
errorStrategy = 'ignore'
}
withLabel:error_retry {
errorStrategy = 'retry'
maxRetries = 2
}
withLabel:process_gpu {
ext {
use_gpu = { workflow.profile.contains('gpu') }
}
accelerator = { workflow.profile.contains('gpu') ? 1 : null }
}
shell = ['bash', '-C', '-e', '-u', '-o', 'pipefail']
withName:'BIGBIO_QUANTMS:QUANTMS:CUSTOM_DUMPSOFTWAREVERSIONS' {
publishDir = [path:{ "${params.outdir}/pipeline_info" }, mode:'copy', pattern:'*_versions.yml']
}
withName:'BIGBIO_QUANTMS:QUANTMS:SUMMARY_PIPELINE' {
publishDir = [path:{ "${params.outdir}/pmultiqc" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }]
}
withName:'BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK' {
publishDir = [path:{ "${params.outdir}/sdrf" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }]
}
withName:'.*:SDRF_PARSING' {
publishDir = [path:{ "${params.outdir}/sdrf" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }]
}
withName:'.*:MSSTATS_LFQ|MSSTATS_TMT' {
publishDir = [path:{ "${params.outdir}/msstats" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }]
}
withName:'.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER|FINAL_QUANTIFICATION|CONVERT_RESULTS' {
publishDir = [path:{ "${params.outdir}/quant_tables" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }]
}
withName:'.*:PSM_CONVERSION' {
publishDir = [path:{ "${params.outdir}/psm_tables" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }]
}
withName:'.*:FDR_CONSENSUSID' {
ext {
args = '-PSM true -protein false'
}
}
withName:'.*:TMT:.*:ID_MAPPER' {
ext {
args = '-debug 0'
}
}
level = 'proteingroup'
decoys_present = '-remove_decoys'
withName:'.*:TMT:PROTEIN_INFERENCE:ID_FILTER' {
ext {
args = '-score:proteingroup "0.01" -score:psm "0.01" -delete_unreferenced_peptide_hits -remove_decoys'
suffix = '.consensusXML'
}
}
withName:'.*:TMT:PROTEIN_QUANT:PROTEIN_QUANTIFIER' {
ext {
args = '-debug 0'
}
}
withName:'.*:TMT:PROTEIN_QUANT:MSSTATS_CONVERTER' {
ext {
args = '-debug 0'
}
}
withName:'.*:PERCOLATOR' {
ext {
args = '-debug 0'
}
}
withName:'.*:PROTEIN_INFERENCE' {
ext {
args = '-debug 0'
}
}
withName:'.*:ID:PSM_FDR_CONTROL:ID_FILTER' {
ext {
args = '-score:psm "0.10"'
suffix = '.idXML'
}
}
withName:'.*:DDA_ID:PSM_FDR_CONTROL:ID_FILTER' {
ext {
args = '-score:psm "0.10"'
suffix = '.idXML'
}
}
withName:'.*:LFQ:PROTEOMICSLFQ' {
ext {
args = '-debug 0'
}
}
withName:'.*:DIA:INSILICO_LIBRARY_GENERATION' {
ext {
args = '--met-excision'
}
}
withName:'.*:DIA:PRELIMINARY_ANALYSIS' {
ext {
args = '--quick-mass-acc --min-corr 2 --corr-diff 1 --time-corr-only'
}
}
withName:MSRESCORE_FEATURES {
ext {
args = '--ms2_model HCD2021 --calibration_set_size 0.15 --feature_generators deeplc,ms2pip'
}
}
withName:'.*:DDA_ID:PHOSPHO_SCORING:ID_SCORE_SWITCHER' {
ext {
args = '-new_score_orientation lower_better -old_score "q-value" -new_score_type "Posterior Error Probability" -debug 0'
}
}
executor = 'azurebatch'
queue = 'pool-pxd040621-heweb'
}
apptainer {
registry = 'quay.io'
enabled = false
}
docker {
registry = 'quay.io'
enabled = true
runOptions = '-u $(id -u):$(id -g)'
}
podman {
registry = 'quay.io'
enabled = false
}
singularity {
registry = 'quay.io'
enabled = false
}
charliecloud {
registry = 'quay.io'
enabled = false
}
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = '/.Rprofile'
R_ENVIRON_USER = '/.Renviron'
JULIA_DEPOT_PATH = '/usr/local/share/julia'
}
nextflow {
enable {
configProcessNamesValidation = false
}
}
timeline {
enabled = true
file = 'timeline-3i5kEjsJrY9iFc.html'
}
report {
enabled = true
file = 'az://pxd040621-heweb/PXD040621/results-demo-compenv/pipeline_info/execution_report_2025-11-26_15-18-50.html'
}
trace {
enabled = true
file = 'az://pxd040621-heweb/PXD040621/results-demo-compenv/pipeline_info/execution_trace_2025-11-26_15-18-50.txt'
}
dag {
enabled = true
file = 'az://pxd040621-heweb/PXD040621/results-demo-compenv/pipeline_info/pipeline_dag_2025-11-26_15-18-50.html'
}
manifest {
name = 'bigbio/quantms'
homePage = 'https://github.com/bigbio/quantms'
contributors = [[name:'Yasset Perez-Riverol', affiliation:'European Bioinformatics Institute (EMBL-EBI), Cambridge, UK', email:'ypriverol@gmail.com', github:'ypriverol', contribution:['maintainer', 'author'], orcid:'0000-0001-6579-6941'], [name:'Dai Chengxin', affiliation:'State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, Beijing, China', email:'daichengxin999@gmail.com', github:'daichengxin', contribution:['author', 'maintainer'], orcid:'0000-0001-6943-5211'], [name:'Julianus Pfeuffer', affiliation:'Algorithmic Bioinformatics, Freie Universität Berlin, Berlin, Germany', email:'jule.pf@gmail.com', github:'jpfeuffer', contribution:['author', 'maintainer'], orcid:'0000-0001-8948-9209'], [name:'Dongze He', affiliation:'Altos Labs, Inc.', email:'dongzehe.zaza@gmail.com', github:'DongzeHe', contribution:['contributor'], orcid:'0000-0001-8259-7434'], [name:'Henry Webel', affiliation:'DTU biosustain, Technical University of Denmark, Lyngby, Denmark', email:'heweb@dtu.dk', github:'enryh', contribution:['contributor'], orcid:'0000-0001-8833-7617'], [name:'Fabian Egli', github:'fabianegli', contribution:['contributor'], orcid:'0000-0001-5294-401X']]
description = 'Quantitative Mass Spectrometry nf-core workflow'
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.10.5'
version = '1.6.0'
doi = '10.5281/zenodo.15573386'
}
plugins = ['nf-schema@2.4.2']
validation {
defaultIgnoreParams = ['genomes']
monochromeLogs = false
help {
enabled = true
command = 'nextflow run bigbio/quantms -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>'
fullParameter = 'help_full'
showHiddenParameter = 'show_hidden'
beforeText = '
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m bigbio/quantms 1.6.0[0m
-[2m----------------------------------------------------[0m-
'
afterText = '
* The pipeline
https://doi.org/10.5281/zenodo.15573386
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/bigbio/quantms/blob/master/CITATIONS.md
'
}
summary {
beforeText = '
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m bigbio/quantms 1.6.0[0m
-[2m----------------------------------------------------[0m-
'
afterText = '
* The pipeline
https://doi.org/10.5281/zenodo.15573386
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/bigbio/quantms/blob/master/CITATIONS.md
'
}
}
conda {
enabled = false
}
shifter {
enabled = false
}
azure {
storage {
accountName = 'stheweba6bed813'
}
batch {
location = 'westeurope'
accountName = 'batchpxd040621'
copyToolInstallMode = 'task'
autoPoolMode = false
allowPoolCreation = false
pools {
'pool-pxd040621-heweb' {
vmType = 'standard_d4s_v3'
vmCount = 0
}
}
}
managedIdentity {
clientId = '50eae5e0-e75f-4bd4-a965-8a78b9a7587a'
}
}
workDir = 'az://pxd040621-heweb/scratch/3i5kEjsJrY9iFc'
runName = 'hungry_stallman'
tower {
enabled = true
endpoint = 'https://api.cloud.seqera.io'
}
cloudcache {
enabled = true
path = 'az://pxd040621-heweb/.cache'
}
Slide decks#
The proteomics data analysis course has a set of slides with a quantms section. see pdf
Latest version can be found on course website: dsp_course_proteomics_intro/