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.

type: string
pattern: ^\S+\.csv$

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

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
hidden
type: boolean
default: true

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/

Define pipeline options.

Minimum length of produced peptides.

type: integer
default: 9

Maximum length of produced peptides.

type: integer
default: 11

Only takes effect for pred_method 'syfpeithi'. Allow all peptide lengths within the range of min_pep_len to max_pep_len without reducing them to the matching allele models.

hidden
type: boolean

Epitope prediction method to use

type: string

Threshold for binder/non-binder calling when using SYFPEITHI epitope prediction method.

hidden
type: number
default: 0.5

Threshold for binder/non-binder calling when using MHCflurry or MHCnuggets epitope prediction methods. The default value of 0.426 corresponds to an IC50 of ≤500.

hidden
type: number
default: 0.426

Display supported alleles of all prediction methods and exit.

type: boolean

Prodigal mode, ‘meta’ or ‘single’.

type: string
default: meta

Enables “deep” memory usage output for main DataFrames generated in pandas scripts (“deep” ensures accurate usage values, but slightly increases runtime).

hidden
type: boolean

Maximum chunk size (#peptides) for epitope prediction jobs.

type: integer
default: 4000000

Scaling factor for prediction_chunk_size parameter for usage in python scripts to reduce memory usage when handling DataFrames.

hidden
type: integer
default: 10

Maximum chunk size (#epitope predictions) for processing of downstream visualisations.

type: integer
default: 7500000

Maximum number of tasks submitted by PREDICT_EPITOPES process

type: integer
default: 1000

Number of files, which are merged in MERGE_PREDICTION_BUFFER

hidden
type: integer
default: 1000

Do not display mean comparison p-values in boxplots.

type: boolean