nf-core/macproqc pipeline parameters

A workflow for the quality control of mass spectrometry-based proteomics analyses

Input/output options

Define where the pipeline should find input data and save output data.

Parameter	Description	Type	Default	Required	Hidden
input	Path to comma-separated file containing information about the samples in the experiment. Help You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.	string		True
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.	string		True
email	Email address for completion summary. Help Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.	string

FASTA parameters

Database settings, to specify the FASTA, create decoys, ...

Parameter	Description	Type	Default	Required	Hidden
fasta	Global input FASTA protein database Help Path to a single protein database file applied to all MS runs. Whether the file already contains decoys is controlled by --skip_decoy_generation.	string		True
skip_decoy_generation	Add this parameter when you want to skip the generation of the decoy database. Help If you want to use your own decoys, you can specify a dataset that includes decoy sequences.	boolean
decoy_string	String that is combined with the accession of the protein identifier to indicate a decoy protein. Help This is passed to the decoy generation as well as to tools using this. Usually, this is a prefix of the protein accession.	string	DECOY_
decoy_method	Method used to generate decoy sequences. (accepted: reverse|shuffle) Help Passed directly to OpenMS DecoyDatabase. Valid values are 'reverse' (default) and 'shuffle'. Has no effect when --skip_decoy_generation is set.	string	reverse
save_decoy_database	Set this parameter to true to save the generated decoy database (for later usage).	boolean

Identification parameters

Search engine specific settings and general settings for the identification of peptides and proteins in MS data. Additional untypical parameters can be adjucted by the modules.config, see there for reference.

Parameter	Description	Type	Default	Required	Hidden
comet_config_template	This is the default comet parameters file. In this file, parameters can be set, which are neither passed by common runtime (threads, fasta, ...) or by common search engine parameters. If not set or null, the provided default in assets is used.	string
peptide_mass_tolerance_upper	Comet parameter: peptide_mass_tolerance_upper, upper bound of the precursor mass tolerance	number	5.0
peptide_mass_tolerance_lower	Comet parameter: peptide_mass_tolerance_lower, lower bound of the precursor mass tolerance; USUALLY NEGATIVE TO BE LOWER THAN 0	number	-5.0
peptide_mass_units	Comet parameter: peptide_mass_units, 0=amu, 1=mmu, 2=ppm	integer	2
isotope_error	Comet parameter: isotope_error, 0=off, 1=0/1 (C13 error), 2=0/1/2, 3=0/1/2/3, 4=-1/0/1/2/3, 5=-1/0/1	integer	2
fragment_bin_tol	Comet parameter: fragment_bin_tol, binning to use on fragment ions	number	0.02
fragment_bin_offset	Comet parameter: fragment_bin_offset, offset position to start the binning (0.0 to 1.0)	number	0.0
theoretical_fragment_ions	Comet parameter: theoretical_fragment_ions, 0=use flanking peaks, 1=M peak only	integer	0
psms_per_spectrum	Comet parameter: num_output_lines: num peptide results to show	integer	5
variable_modifications	Comet parameter: adjust or add the variable modifications to overwrite in the template. The actual string MUST be in single quotes inside a string, like "'variable_mod01 = 15.9949 M 0 3 -1 0 0 0.0'". Variables are defined like in the comet params file (with 'variable_modXX = ...'). Multiple modifications can be defined by separating them with a semicolon.	string
static_modifications	Comet parameter: set the variable modifications to overwrite in the template.The actual string MUST be in single quotes inside a string, like "'add_C_cysteine = 57.021464'". The variables are defined like in the comet params file (with 'add_XX_... = ...'). Multiple modifications can be defined by separating them with a semicolon.	string
label_modifications	Additional Comet static modifications appended only for the labelled COMETCONFIG search. Use the same syntax as static_modifications, for example "'add_K_lysine = 8.014199;add_R_arginine = 10.008269'".	string
pia_fdr_threshold	FDR threshold used by PIA for the final PSM-, peptide- and protein-level filtering.	number	0.01
pia_prefilter_threshold	FDR threshold used by PIA's optional PSM-level pre-filtering pass, run before the final --pia_fdr_threshold analysis on the unlabelled search to speed up the total time and reduce the memory consumption for the whole analysis. Set to 0 to disable pre-filtering.	number	0.05

Visualization parameters

Parameters for the visualization of the QC results.

Parameter	Description	Type	Default	Required	Hidden
figure_format	Output format for figures (plotly, html, or both as 'html,plotly') (accepted: plotly|html|html,plotly)	string	plotly
output_table_type	Output format for the summary table (accepted: csv|tsv|xlsx)	string	csv
spikeins	Whether spike-ins were included in the analysis. If information on identified spike-in peptides is available (spikeins = true), they can be included in the summary table and the calculation of the principle component analysis (PCA).	boolean	True
rt_unit	Unit for retention time in plots ('min', 'sec'). (accepted: sec|min)	string	sec
output_column_order	Order of columns for the output table, separated by commas, e.g. 'filename,startTime,nr_MS1,nr_MS2'.	string	None
spikein_columns	Spike-in columns to include in the output table, separated by commas. Available columns: 'MS1 feature maximum intensity' (maximum XIC intensity observed for the spike-in peptide), 'retention time' (observed retention time at that maximum intensity), 'count of identified spectra' (number of identified spectra/PSMs matching the spike-in peptide), 'predicted retention time' (expected retention time from the spike-ins reference table), and 'Delta_to_expected_RT' (difference between observed and predicted retention time).	string	MS1 feature maximum intensity,retention time,count of identified spectra,Delta_to_expected_RT
height_barplots	Height of the bar plots in pixels.	integer	700
width_barplots	Width of the bar plots in pixels. Default = 0 means automatic width.	integer	0
height_pca	Height of the PCA plots in pixels.	integer	1000
width_pca	Width of the PCA plots in pixels.	integer	1000
height_ionmaps	Height of the ion maps plots in inches.	number	10.0
width_ionmaps	Width of the ion maps plots in inches.	number	10.0
spike_ins_table	Spike-ins reference table as a csv file. Please refer to the usage docs for details on the required format and columns.	string	None

Institutional config options

Parameters used to describe centralised config profiles. These should not be edited.

Parameter	Description	Type	Default	Required	Hidden
custom_config_version	Git commit id for Institutional configs.	string	master		True
custom_config_base	Base directory for Institutional configs. Help If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.	string	https://raw.githubusercontent.com/nf-core/configs/master		True
config_profile_name	Institutional config name.	string			True
config_profile_description	Institutional config description.	string			True
config_profile_contact	Institutional config contact information.	string			True
config_profile_url	Institutional config URL link.	string			True

Generic options

Less common options for the pipeline, typically set in a config file.

Parameter	Description	Type	Default	Required	Hidden
version	Display version and exit.	boolean			True
publish_dir_mode	Method used to save pipeline results to output directory. (accepted: symlink|rellink|link|copy|copyNoFollow|move) Help The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.	string	copy		True
email_on_fail	Email address for completion summary, only when pipeline fails. Help An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.	string			True
plaintext_email	Send plain-text email instead of HTML.	boolean			True
monochrome_logs	Do not use coloured log outputs.	boolean			True
validate_params	Boolean whether to validate parameters against the schema at runtime	boolean	True		True
pipelines_testdata_base_path	Base URL or local path to location of pipeline test dataset files	string	https://raw.githubusercontent.com/nf-core/test-datasets/		True
macproqc_testdata_base_path	Base URL or local path to location of specific macproqc test dataset files	string	https://raw.githubusercontent.com/mpc-bioinformatics/macproqc-test-data/main/testdata/		True
trace_report_suffix	Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.	string			True
help	Display the help message.	['boolean', 'string']
help_full	Display the full detailed help message.	boolean
show_hidden	Display hidden parameters in the help message (only works when --help or --help_full are provided).	boolean