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)

required
type: string
pattern: ^\S+\.tsv$

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Email address for completion summary.

type: string
pattern: ^([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.

type: string

Input FASTA protein database

type: string
pattern: .fasta$

Set depending on whether variants should be translated to proteins and included into your fasta for database search.

type: boolean

Add 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

type: boolean

Specify the MS levels for which the peak picking is applied (unless you use --run_centroidisation).

type: integer
default: 2

Include the flag when the specified ms level is not centroided (default=false).

type: boolean

Specify the minimum length of peptides to be considered after processing

type: integer
default: 8

Specify the maximum length of peptides to be considered after processing

type: integer
default: 12

Specify the fragment mass tolerance to be used for the comet database search.

type: number
default: 0.02

Specify the precursor mass tolerance to be used for the comet database search.

type: integer
default: 5

Specify the fragment bin offset to be used for the comet database search.

type: number

Specify the maximum number of modifications that should be contained in a peptide sequence match.

type: integer
default: 3

Specify the number of hits that should be reported for each spectrum.

type: integer
default: 1

Specify the mass range that peptides should fulfill to be considered for peptide spectrum matching.

type: string
default: 800:2500

Specify the precursor charge range that peptides should fulfill to be considered for peptide spectrum matching.

type: string
default: 2:3

Specify which fragmentation method was used in the MS acquisition

type: string

Specify which enzymatic restriction should be applied

hidden
type: string
default: unspecific cleavage

Set a maximum retention time shift for the linear rt alignment

type: integer
default: 300

Specify which fixed modifications should be applied to the database search

type: string

Specify which variable modifications should be applied to the database search

type: string
default: Oxidation (M)

Include x ions into the peptide spectrum matching

type: boolean

Include z ions into the peptide spectrum matching

type: boolean

Include a ions into the peptide spectrum matching

type: boolean

Include c ions into the peptide spectrum matching

type: boolean

Include NL ions into the peptide spectrum matching

type: boolean

Include if you want to remove all peaks around precursor m/z

type: boolean

Size of Spectrum batch for Comet processing (Decrease/Increase depending on Memory Availability)

type: integer

Specify a .tsv file containing the information about genomic variants (vcf files < v.4.2) for each sample.

type: string
pattern: ^\S+\.tsv$

Set this option to create documents that are created to perform the ion annotation

type: boolean
default: false

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

type: string
default: high_res

Default Comet params file. All parameters of this take precedence.

type: string

Clean up mzml files and remove artificial charge 0 peptides.

type: boolean

Specify the level at which the false discovery rate should be computed.

type: string

Specify the false discovery rate threshold at which peptide hits should be selected.

type: number
default: 0.01

Set if MHCquant should be run in SubsetFDR mode

type: boolean

Affinity threshold (nM) used to define binders for PSM subset selection in the FDR refinement procedure

type: integer
default: 500

Specify percolator descriptor feature set

type: integer

Use klammer retention time features for Percolator rescoring

type: boolean

Maximum subset for percolator training iterations

type: integer

Use DeepLC retention time features for Percolator rescoring

type: boolean

Number of bins (peptides) used for DeepLC calibration. For each bin the best hit is used.

type: integer

Specify 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

type: string

Add absolute RT error to of experimental and predicted RT to the feature set

type: boolean

Add squared RT error to of experimental and predicted RT to the feature set

type: boolean

Add log RT error to of experimental and predicted RT to the feature set

type: boolean

Use MS2pip peak intensity prediction for Percolator rescoring

type: boolean

Skip quantification and only yield peptide identifications

type: boolean

Compute FDR for the targeted approach

type: boolean

Specify a cut off probability value for quantification events as a filter

type: number

Specify a m/z window for matching between runs

type: number

Specify a rt window for matching between runs

type: number

Specify a rt mapping tolerance for mapping features between runs

type: number

Specify a peak width for feature extraction

type: number

Specify a minimum peak width for quantification

type: number

Specify a .tsv file containing the MHC alleles of your probes as well as their metadata such as SampleID.

type: string
pattern: ^\S+\.tsv$

Set flag depending on whether MHC class 1 binding predictions using the tool mhcflurry should be run.

type: boolean

Set flag depending on whether MHC class 2 binding predictions using the tool mhcnuggets should be run.

type: boolean

Specify genomic reference used for variant annotation

type: string

Specify style of tool used for variant annotation - currently supported

type: string

Set this option to not consider insertions and deletions for variant translation

type: boolean

Set this option to not consider frameshifts for variant translation

type: boolean

Set this option to not consider snps for variant translation

type: boolean

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Skip MultiQC.

hidden
type: boolean

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^[\d\.]+\s*.(K|M|G|T)?B$

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean