Define where the pipeline should find input data and save output data.

Path to comma-separated file containing information about the samples in the experiment.

required
type: string

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

Options for the genome and proteome reference.

Specifies the Ensembl genome reference version that will be used.

type: string
default: grch37

Specifies the reference proteome fasta file that is used for self-filtering peptides derived from provided genomic variants.

type: string

Options for the peptide prediction step.

Specifies the column name in the input file that contains the peptide sequences.

type: string
default: sequence

Specifies the minimum peptide length.

type: integer
default: 8

Specifies the maximum peptide length.

type: integer
default: 12

Specifies the minimum peptide length for MHC class II peptides.

type: integer
default: 8

Specifies the maximum peptide length for MHC class II peptides.

type: integer
default: 25

Specifies the prediction tool(s) to use.

type: string
default: mhcnuggets

Specifies whether wild-type sequences should be predicted.

type: boolean

Specifies that sequences of proteins, affected by provided variants, will be written to a FASTA file.

type: boolean

Specifies the size of the flanking regions around a mutation in a peptide in the FASTA file (if fasta_output is set to true).

hidden
type: integer
default: 25

Specifies that the output file will be in wide format.

type: boolean

Options for optimising the pipeline run execution.

Split VCF file into multiple files by number of variants.

type: boolean

Number of variants that should be written into one file. Default: number of variants divided by ten

hidden
type: integer

Number of nucleotides between previous and current variant across split.

hidden
type: integer
default: 110000

Specifies the maximum number of peptide chunks.

type: integer
default: 100

Specifies the minimum number of peptides that should be written into one chunk.

type: integer
default: 5000

External MHC binding prediction software that is not shipped with the pipeline.

Specifies the path to the JSON file with meta information on external prediction tools.

hidden
type: string

Specifies the operating system in use (Linux or Darwin). This is only necessary if conda is used.

type: string

To use the ‘netmhcpan’ tool, specify the path to the original software tarball for NetMHCpan 4.0 here.

type: string
pattern: ^\S+\.tar\.gz$

To use the ‘netmhciipan’ tool, specify the path to the original software tarball for NetMHCIIpan 3.1 here.

type: string
pattern: ^\S+\.tar\.gz$

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