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.
stringInput FASTA protein database
string.fasta$If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible.
Set depending on whether variants should be translated to proteins and included into your fasta for database search.
booleanAdd this parameter when you want to skip the generation of the decoy database, the consequence is that it prevents the generation of variants and FDR refinement
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_'.
One should consider though that this option will then prevent appending variants to the database and if not using reversed decoys the subset refinement FDR option will not work.
Specify the MS levels for which the peak picking is applied (unless you use --run_centroidisation).
integer2Include the flag when the specified ms level is not centroided (default=false).
booleanSpecify the minimum length of peptides to be considered after processing
integer8Specify the maximum length of peptides to be considered after processing
integer12Specify the fragment mass tolerance to be used for the comet database search.
number0.02For High-Resolution instruments a fragment mass tolerance value of 0.02 is recommended. (See the Comet parameter documentation: eg. 0.02)
Specify 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 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: eg. 0)
Specify the maximum number of modifications that should be contained in a peptide sequence match.
integer3Specify the number of hits that should be reported for each spectrum.
integer1Specify the mass range that peptides should fulfill to be considered for peptide spectrum matching.
string800:2500Specify the precursor charge range that peptides should fulfill to be considered for peptide spectrum matching.
string2:3Specify which fragmentation method was used in the MS acquisition
stringSpecify which enzymatic restriction should be applied
stringunspecific cleavagefor HLA peptides rarely other enzymes are used, however most enzymes such as for example 'Trypsin' are available (see OpenMS enzymes)
Set a maximum retention time shift for the linear rt alignment
integer300Specify 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)
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)
Include 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 a .tsv file containing the information about genomic variants (vcf files < v.4.2) for each sample.
string^\S+\.tsv$| Sample | VCF_FileName |
| -------------| :---------------------:|
| MM15_Melanom | data/MM15_variants.vcf |
| MM17_Melanom | data/MM17_variants.vcf |
Set this option to create documents that are created to perform the ion annotation
booleanfalseComets 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
stringhigh_resDefault Comet params file. All parameters of this take precedence.
stringClean up mzml files and remove artificial charge 0 peptides.
booleanSpecify the level at which the false discovery rate should be computed.
stringSpecify the false discovery rate threshold at which peptide hits should be selected.
number0.01Set if MHCquant should be run in SubsetFDR mode
booleanSubsetFDR makes use of binding predictions applying the tool mhcflurry to subset all PSMs not passing the q-value threshold. If specified the FDR will be refined using Percolator on the subset of predicted binders among all PSMs resulting in an increased identification rate. (Please be aware that this option is only available for MHC class I data of alleles that are supported by mhcflurry)
Affinity threshold (nM) used to define binders for PSM subset selection in the FDR refinement procedure
integer500Specify percolator descriptor feature set
integerSee percolator description (https://github.com/percolator/percolator/wiki/Retention-time-and-calibration)
Use klammer retention time features for Percolator rescoring
booleanhttps://pubs.acs.org/doi/10.1021/ac070262k
Maximum subset for percolator training iterations
integerUse DeepLC retention time features for Percolator rescoring
booleanhttps://www.nature.com/articles/s41592-021-01301-5
Number of bins (peptides) used for DeepLC calibration. For each bin the best hit is used.
integerSpecify the DeepLC calibration mode. rt_bin: bin peptides by RT, idx_bin: bin peptides by index, min_max: scale uncalibrated predictions to experimental RT range
stringAdd absolute RT error to of experimental and predicted RT to the feature set
booleanAdd squared RT error to of experimental and predicted RT to the feature set
booleanAdd log RT error to of experimental and predicted RT to the feature set
booleanUse MS2pip peak intensity prediction for Percolator rescoring
booleanhttps://github.com/compomics/ms2pip
MS2pip model name defined (https://github.com/compomics/ms2pip#specialized-prediction-models)
stringSkip quantification and only yield peptide identifications
booleanCompute 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
numberSpecify a rt window for matching between runs
numberSpecify a rt mapping tolerance for mapping features between runs
numberSpecify a peak width for feature extraction
numberSpecify a minimum peak width for quantification
numberSpecify a .tsv file containing the MHC alleles of your probes as well as their metadata such as SampleID.
string^\S+\.tsv$| Sample | HLA_Alleles_Class_1 | HLA_Alleles_Class_2 |
| -------------| :----------------------------------------------:| ------------------------------------------:|
| MM15_Melanom | A*03:01;A*68:01;B*27:05;B*35:03;C*02:02;C*04:01 | HLA-DRB1*01:01;HLA-DQB1*03:19;HLA-DQA1*05:01 |
| MM17_Melanom | A*02:01;B*07:01;B*26:01;C*11:01;C*01:01 | HLA-DRB1*01:02;HLA-DRB3*02:02;HLA-DRB4*01:03 |
Set flag depending on whether MHC class 1 binding predictions using the tool mhcflurry should be run.
booleanSet flag depending on whether MHC class 2 binding predictions using the tool mhcnuggets should be run.
booleanSpecify genomic reference used for variant annotation
stringSpecify style of tool used for variant annotation - currently supported
stringSet this option to not consider insertions and deletions for variant translation
booleanSet this option to not consider frameshifts for variant translation
booleanSet this option to not consider snps for variant translation
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterSkip MultiQC.
booleanBase 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.