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

Decoy Database generation settings

Input FASTA protein database

required
type: string
pattern: .fasta$

Add this parameter when you want to skip the generation of the decoy database.

type: boolean

Define pre-search settings

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

type: boolean

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

type: integer
default: 2

Clean up spectrum files and remove artificial charge 0 peptides.

type: boolean

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

Specify which enzymatic restriction should be applied

hidden
type: string

Specify which fragmentation method was used in the MS acquisition

type: string

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

type: string

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

type: string

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

type: integer
default: 5

Specify the unit of the precursor mass tolerance to be used for the Comet database search.

type: string

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

type: number

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

type: number
default: 0.01

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

type: integer
default: 3

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)

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

type: integer
default: 1

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
default: false

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

hidden
type: integer

Specify custom Comet params file. All parameters of this take precedence.

hidden
type: string

Specify the rescoring engine that should be used for rescoring. Either percolator or mokapot

type: string

Specify the feature generator that should be used for rescoring. One or multiple of basic,ms2pip,deeplc,ionmob

type: string
default: deeplc,ms2pip

Specify the MS²PIP model that should be used for rescoring. Checkout the MS²PIP documentation for available models.

type: string

Specify a local directory holding at least the MS²PIP models specified in ms2pip_model.

hidden
type: string

Specify the number or percentage of PSMs that should be used for calibration of the DeepLC model.

hidden
type: number
default: 0.15

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

Compute global FDR and backfilter sample-specific FDRs

type: boolean

Maximum subset for Percolator training iterations

hidden
type: integer

Turn on quantification mode

type: boolean

Set a maximum retention time shift for the linear RT alignment

type: integer
default: 300

Compute FDR for the targeted approach

hidden
type: boolean

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

hidden
type: number

Specify a m/z window for matching between runs

hidden
type: number
default: 5

Specify a rt window for matching between runs

hidden
type: number

Specify a rt mapping tolerance for mapping features between runs

hidden
type: number

Specify a peak width for feature extraction

hidden
type: number
default: 60

Specify a minimum peak width for quantification

hidden
type: number
default: 0.2

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

Generate 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.

type: boolean

Create tsv files containing information about the MS2 ion annotations after processing.

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

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

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

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

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://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.

hidden
type: string