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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringDecoy Database generation settings
Input FASTA protein database
string.fasta$Add this parameter when you want to skip the generation of the decoy database.
booleanDefine pre-search settings
Include the flag when the specified ms level is not centroided (default=false).
booleanSpecify the MS levels for which the peak picking is applied (unless you use --run_centroidisation).
integer2Clean up spectrum files and remove artificial charge 0 peptides.
booleanComets 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
stringSpecify which enzymatic restriction should be applied
stringSpecify which fragmentation method was used in the MS acquisition
stringSpecify the mass range in Dalton that peptides should fulfill to be considered for peptide spectrum matching.
stringSpecify the precursor charge range that peptides should fulfill to be considered for peptide spectrum matching.
stringSpecify the precursor mass tolerance to be used for the Comet database search.
integer5Specify the unit of the precursor mass tolerance to be used for the Comet database search.
stringSpecify the fragment bin offset to be used for the comet database search.
numberSpecify the fragment mass tolerance to be used for the comet database search.
number0.01Specify the maximum number of modifications that should be contained in a peptide sequence match.
integer3Specify which fixed modifications should be applied to the database search
stringSpecify which variable modifications should be applied to the database search
stringOxidation (M)Specify the number of hits that should be reported for each spectrum.
integer1Include x ions into the peptide spectrum matching
booleanInclude z ions into the peptide spectrum matching
booleanInclude a ions into the peptide spectrum matching
booleanInclude c ions into the peptide spectrum matching
booleanInclude NL ions into the peptide spectrum matching
booleanInclude if you want to remove all peaks around precursor m/z
booleanfalseSize of Spectrum batch for Comet processing (Decrease/Increase depending on Memory Availability)
integerSpecify custom Comet params file. All parameters of this take precedence.
stringSpecify the rescoring engine that should be used for rescoring. Either percolator or mokapot
stringSpecify the feature generator that should be used for rescoring. One or multiple of basic,ms2pip,deeplc,ionmob
stringdeeplc,ms2pipSpecify the MS²PIP model that should be used for rescoring. Checkout the MS²PIP documentation for available models.
stringSpecify a local directory holding at least the MS²PIP models specified in ms2pip_model.
stringSpecify the number or percentage of PSMs that should be used for calibration of the DeepLC model.
number0.15Specify the level at which the false discovery rate should be computed.
stringSpecify the false discovery rate threshold at which peptide hits should be selected.
number0.01Compute global FDR and backfilter sample-specific FDRs
booleanMaximum subset for Percolator training iterations
integerTurn on quantification mode
booleanSet a maximum retention time shift for the linear RT alignment
integer300Compute FDR for the targeted approach
booleanSpecify a cut off probability value for quantification events as a filter
numberSpecify a m/z window for matching between runs
number5Specify a rt window for matching between runs
numberSpecify a rt mapping tolerance for mapping features between runs
numberSpecify a peak width for feature extraction
number60Specify a minimum peak width for quantification
number0.2Specify the minimum length of peptides to be considered after processing
integer8Specify the maximum length of peptides to be considered after processing
integer12Generate 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.
booleanCreate tsv files containing information about the MS2 ion annotations after processing.
booleanParameters 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.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
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.
string