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$

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.

required
type: string

Email address for completion summary.

type: string
pattern: ^([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.

type: string

Decoy Database generation settings

Input FASTA protein database

required
type: string
pattern: .fasta$

Path to the protein database file

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

type: boolean

If 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).

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

hidden
type: string

Specify which enzymatic restriction should be applied

hidden
type: string

For 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

type: string

If 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.

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

For 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.

type: string

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

hidden
type: number

For 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.

type: number
default: 0.01

For 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.

type: integer
default: 3

Specify which fixed modifications should be applied to the database search

type: string

e.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

type: string
default: Oxidation (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.

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

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

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

(Weisser H. and Choudhary J.S. J Proteome Res. 2017 Aug 4)

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

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

type: boolean

The 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.

hidden
type: string
default: master

Base directory for Institutional configs.

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

If 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.

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

Use 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.

hidden
type: string
default: 128.GB
pattern: ^[\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.

hidden
type: string
default: 240.h
pattern: ^(\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.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

The 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.

hidden
type: string
pattern: ^([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.

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

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

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

By 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.

hidden
type: boolean

By default, when an unrecognised parameter is found, it returns a warinig.

Validation of parameters in lenient more.

hidden
type: boolean

Allows 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

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/