nf-core/mspepid
This pipeline performs the peptide identification of MS2 spectra from a proteomics experiment. For this, different search algorithm and rescoring approaches can be selected.
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Database settings, to specify the FASTA, create decoys and entrapments
Input FASTA protein database
string.(fasta|faa)$This parameter specifies for an entrapment search the fold of entrapment proteins per target protein. No database will be created if 0.
integerAdd this parameter when you want to skip the generation of the decoy database.
booleanSearch parameters that are common to all search engines.
The precursor tolerance in PPM
integer10The fragment tolerance in Dalton
number0.02Search parameters specific to Sage
Path to the Sage params file. If not set or null, the provided default in assets is used.
stringWhether the database should be split during Sage search. This greatly reduces memory consumption when using large databases (beta feature)
booleanNumber of proteins per database chunk when prefiltering is active.
integerEnable/disable search engines.
Enables spectrum identification with Comet.
booleantrueEnables spectrum identification with Sage.
booleantrueThis 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.
stringEnable/disable rescoring algorithms.
Enables rescoring with Percolator. Some rescorings (MS2Rescore, Oktoberfest) depend on Percolator results, so Percolator will be run if any of these are enabled, even if this parameter is set to false.
booleantrueEnables rescoring with MS2Rescore.
booleantrueThe MS2PIP model to use for MS2Rescore. Models can be found here: https://ms2pip.readthedocs.io/en/latest/prediction-models/
stringHCDOptional directory with pre-downloaded MS2PIP model files. If set to null, the respective model is downloaded and saved in the results directory.
stringParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringDisplay the help message.
boolean,stringDisplay the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when —help or —help_full are provided).
boolean