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	Required
`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
`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
`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`

Institutional config options¶

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

Parameter	Description	Type	Default	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	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`