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

Use this to specify a sample sheet table including your input raw or mzml files as well as their metainformation 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.

type: string
default: ./results

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.

Input FASTA protein database

type: string

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

Set depending on whether own decoy database should be used

type: boolean

If you want to use your own decoys, you can specify a databaset that includes decoy sequences. However, each database entry should keep the prefix 'DECOY_'.
One should consider though that this option will then prevent to append variants to the database and if not using reversed decoys the subset refinement FDR option will not work.

If one ms level in the raw ms data is not centroided, specify the level here. (eg. 2)

type: integer
default: 2

Choose whether the specified ms_level in pick_ms_levels is centroided or not.

type: boolean

Specify the minimum length of peptides considered after processing

type: integer
default: 8

Specify the maximum length of peptides considered after processing

type: integer
default: 12

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

type: number
default: 0.02

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 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 used for the comet database search.

type: integer

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 fullfill to be considered for peptide spectrum matching.

type: string
default: 800:2500

Specifiy the precursor charge range that peptides should fullfill 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)

Specify which variable modifications should be applied to the database search

type: string
default: Oxidation (M)

e.g. 'Oxidation (M)' (see OpenMS modifications)

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 precursor ions into the peptide spectrum matching

type: boolean
default: true

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

type: integer
default: 500

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

type: string

| Sample | VCF_FileName |
| -------------| :---------------------:|
| MM15_Melanom | data/MM15_variants.vcf |
| MM17_Melanom | data/MM17_variants.vcf |

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

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: string

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

type: string

| 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

Specify whether insertions and deletions should not be considered for variant translation

type: boolean
default: true

Specify whether frameshifts should not be considered for variant translation

type: boolean
default: true

Specify whether snps should not be considered for variant translation

type: boolean

Set this option to predict retention times of all identified peptides and possible neoepitopes based on high scoring ids

type: boolean

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

Display help text.

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.

Workflow name.

hidden
type: string

A custom name for the pipeline run. Unlike the core nextflow -name option with one hyphen this parameter can be reused multiple times, for example if using -resume. Passed through to steps such as MultiQC and used for things like report filenames and titles.

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})$

This works exactly as with --email, except emails are only sent if the workflow is not successful.

Send plain-text email instead of HTML.

hidden
type: boolean

Set to receive plain-text e-mails instead of HTML formatted.

Do not use coloured log outputs.

hidden
type: boolean

Set to disable colourful command line output and live life in monochrome.

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

Options for the reference genome indices used to align reads.

Do not load the iGenomes reference config.

hidden
type: boolean

Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.

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

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

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'

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

Git commit id for Institutional configs.

hidden
type: string
default: master

Provide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.

## Download and use config file with following git commit id  
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96  

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 the custom_config_base option. For example:

## Download and unzip the config files  
cd /path/to/my/configs  
wget https://github.com/nf-core/configs/archive/master.zip  
unzip master.zip  
  
## Run the pipeline  
cd /path/to/my/data  
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/  

Note that the nf-core/tools helper package has a download command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.

Institutional configs hostname.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string