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$Use this to specify a sample sheet table including your input raw or mzml files as well as their meta information such as SampleID and Condition. For example:
| ID | Sample | Condition | ReplicateFileName |
| -----|:------------:| ----------:|------------------------------------------:|
| 1 | MM15_Melanom | A | data/MM15_Melanom_W_1_A_standard.raw |
| 2 | MM15_Melanom | B | data/MM15_Melanom_W_1_B_standard.raw |
| 3 | MM17_Melanom | B | data/MM17_Melanom_W_1_B_standard.raw |
--input 'path/samples.tsv'
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringDecoy Database generation settings
Input FASTA protein database
string.fasta$Path to the protein database file
Add this parameter when you want to skip the generation of the decoy database.
booleanIf you want to use your own decoys, you can specify a dataset that includes decoy sequences. However, each database entry should keep the prefix 'DECOY_'.
Define 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
stringFor HLA peptides rarely other enzymes are used, however most enzymes such as for example 'Trypsin' are available.
Specify which fragmentation method was used in the MS acquisition
stringIf not specified, ALL tries to infer the fragmentation method based on the spectrum file
Specify 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.
integer5For high-resolution instruments a precursor mass tolerance value of 5ppm is recommended. (eg. 5)
Specify 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.
numberFor high-resolution instruments a fragment bin offset of 0 is recommended. (See the Comet parameter documentation: https://uwpr.github.io/Comet/parameters/parameters_202401/).
This parameter needs to be combined with fragment_bin_tol parameter
Specify the fragment mass tolerance to be used for the comet database search.
number0.01For high-resolution instruments a fragment mass tolerance value of 0.02 is recommended
(See the Comet parameter documentation: https://uwpr.github.io/Comet/parameters/parameters_202401/).
The OpenCometAdapter mulitplies this parameter with 2 to align with other search engines.
Specify 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
stringe.g. 'Carbamidomethyl (C)' (see OpenMS modifications; for a list of options, see parameter description on https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_CometAdapter.html).
Multiple modifications can be specified by separating commas:Oxidation (M),Carbamidomethyl (C)
Specify which variable modifications should be applied to the database search
stringOxidation (M)e.g. 'Oxidation (M)' (see OpenMS modifications; for a list of options, see parameter description on https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_CometAdapter.html).
Multiple modifications can be specified by separating commas:Oxidation (M),Carbamidomethyl (C)
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
booleanSize 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.
number0.01Maximum 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
boolean(Weisser H. and Choudhary J.S. J Proteome Res. 2017 Aug 4)
Specify 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
integer12Create tsv files containing information about the MS2 ion annotations after processing.
booleanThe resulting tsv files should aid in spectrum validation downstream analyses
Parameters 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/masterIf 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.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^[\d\.]+\s*.(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
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
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/