nf-core/mhcquant
Identify and quantify MHC eluted peptides from mass spectrometry raw data
Define where the pipeline should find input data and save output data.
Input raw / mzML files listed in a tsv file (see help for details)
string
^\S+\.tsv$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Decoy Database generation settings
Input FASTA protein database
string
.fasta$
Add this parameter when you want to skip the generation of the decoy database.
boolean
Define pre-search settings
Include the flag when the specified ms level is not centroided (default=false).
boolean
Specify the MS levels for which the peak picking is applied (unless you use --run_centroidisation
).
integer
2
Clean up spectrum files and remove artificial charge 0 peptides.
boolean
Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high_res: sum of intensities plus flanking bins, ion trap (low_res) ms/ms: sum of intensities of central M bin only
string
Specify which enzymatic restriction should be applied
string
Specify which fragmentation method was used in the MS acquisition
string
Specify the mass range in Dalton that peptides should fulfill to be considered for peptide spectrum matching.
string
Specify the precursor charge range that peptides should fulfill to be considered for peptide spectrum matching.
string
Specify the precursor mass tolerance to be used for the Comet database search.
integer
5
Specify the unit of the precursor mass tolerance to be used for the Comet database search.
string
Specify the fragment bin offset to be used for the comet database search.
number
Specify the fragment mass tolerance to be used for the comet database search.
number
0.01
Specify the maximum number of modifications that should be contained in a peptide sequence match.
integer
3
Specify which fixed modifications should be applied to the database search
string
Specify which variable modifications should be applied to the database search
string
Oxidation (M)
Specify the number of hits that should be reported for each spectrum.
integer
1
Include x ions into the peptide spectrum matching
boolean
Include z ions into the peptide spectrum matching
boolean
Include a ions into the peptide spectrum matching
boolean
Include c ions into the peptide spectrum matching
boolean
Include NL ions into the peptide spectrum matching
boolean
Include if you want to remove all peaks around precursor m/z
boolean
false
Size of Spectrum batch for Comet processing (Decrease/Increase depending on Memory Availability)
integer
Specify custom Comet params file. All parameters of this take precedence.
string
Specify the rescoring engine that should be used for rescoring. Either percolator or mokapot
string
Specify the feature generator that should be used for rescoring. One or multiple of basic,ms2pip,deeplc,ionmob
string
deeplc,ms2pip
Specify the MS²PIP model that should be used for rescoring. Checkout the MS²PIP documentation for available models.
string
Specify a local directory holding at least the MS²PIP models specified in ms2pip_model
.
string
Specify the number or percentage of PSMs that should be used for calibration of the DeepLC model.
number
0.15
Specify the level at which the false discovery rate should be computed.
string
Specify the false discovery rate threshold at which peptide hits should be selected.
number
0.01
Compute global FDR and backfilter sample-specific FDRs
boolean
Maximum subset for Percolator training iterations
integer
Turn on quantification mode
boolean
Set a maximum retention time shift for the linear RT alignment
integer
300
Compute FDR for the targeted approach
boolean
Specify a cut off probability value for quantification events as a filter
number
Specify a m/z window for matching between runs
number
5
Specify a rt window for matching between runs
number
Specify a rt mapping tolerance for mapping features between runs
number
Specify a peak width for feature extraction
number
60
Specify a minimum peak width for quantification
number
0.2
Specify the minimum length of peptides to be considered after processing
integer
8
Specify the maximum length of peptides to be considered after processing
integer
12
Generate a spectral library from the search results. If global_fdr
is specified, an additional global FDR-filtered library is generated from all MSruns in the samplesheet.
boolean
Create tsv files containing information about the MS2 ion annotations after processing.
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://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.
string