nf-core/mhcquant
Identify and quantify MHC eluted peptides from mass spectrometry raw data
2.3.1). The latest
stable release is
3.0.0
.
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.
stringInput FASTA protein database
string.fasta$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
booleanSpecify the MS levels for which the peak picking is applied (unless you use --run_centroidisation).
integer2Choose whether the specified ms_level in pick_ms_levels is centroided or not.
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.
number0.02Specify the precursor mass tolerance to be used for the comet database search.
integer5Specify the fragment bin offset to be used for the comet database search.
integerSpecify 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 cleavageSet a maximum retention time shift for the linear rt alignment
integer300Specify which fixed modifications should be applied to the database search
stringSpecify which variable modifications should be applied to the database search
stringOxidation (M)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)
integer500Specify a .tsv file containing the information about genomic variants (vcf files < v.4.2) for each sample.
string^\S+\.tsv$Specify 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
booleanAffinity threshold (nM) used to define binders for PSM subset selection in the FDR refinement procedure
integer500Specify percolator descriptor feature set
integerUse klammer retention time features for Percolator rescoring
booleanMaximum subset for percolator training iterations
integerSkip quantification and only yield peptide identifications
booleanCompute FDR for the targeted approach
stringSpecify a cut off probability value for quantification events as a filter
numberSpecify a .tsv file containing the MHC alleles of your probes as well as their metadata such as SampleID.
string^\S+\.tsv$Set flag depending on whether MHC class 1 binding predictions using the tool mhcflurry should be run.
booleanSet flag depending on whether MHC class 2 binding predictions using the tool mhcnuggets should be run.
booleanSpecify genomic reference used for variant annotation
stringSpecify style of tool used for variant annotation - currently supported
stringSet this option to not consider insertions and deletions for variant translation
booleanSet this option to not consider frameshifts for variant translation
booleanSet this option to not consider snps for variant translation
booleanSet this option to predict retention times of all identified peptides and possible neoepitopes based on high scoring ids
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterSkip MultiQC.
booleanBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^[\d\.]+\s*.(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^[\d\.]+\.*(s|m|h|d|day)$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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$Do not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean