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

Input FASTA protein database

type: string
pattern: .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.

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

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_'.
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).

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: 0.01

For 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.

type: integer
default: 5

For 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.

type: number

For 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.

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

for 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

type: integer
default: 300

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)

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)

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$

| 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

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

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
default: Immuno-HCD

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

type: number
default: 0.15

Set if MHCquant should be run in SubsetFDR mode

type: boolean

SubsetFDR 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

type: integer
default: 500

Specify percolator descriptor feature set

type: integer

See percolator description (https://github.com/percolator/percolator/wiki/Retention-time-and-calibration)

Use klammer retention time features for Percolator rescoring

type: boolean

https://pubs.acs.org/doi/10.1021/ac070262k

Maximum subset for percolator training iterations

type: integer

Skip quantification and only yield peptide identifications

type: boolean

Compute FDR for the targeted approach

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

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$

| 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.

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

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.