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
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

Options for the genome and proteome reference.

Specifies the human reference genome version.

type: string

Specifies the reference proteome.

type: string

Reference genome related files and options required for the workflow.

Do not load the iGenomes reference config.

hidden
type: boolean

Options for the peptide prediction step.

Filter against human proteome.

type: boolean

Specifies the maximum peptide length.

type: integer
default: 11

Specifies the minimum peptide length.

type: integer
default: 8

Specifies the maximum peptide length for MHC class II peptides.

type: integer
default: 16

Specifies the minimum peptide length for MHC class II peptides.

type: integer
default: 15

Specifies the prediction tool(s) to use.

type: string
default: syfpeithi

Specifies tool-specific binder thresholds in a JSON file. This can be used to override the given default binder threshold values.

type: string

Specifies the affinity metric instead of the rank metric used for determining whether a peptide is considered as a binder.

type: boolean

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

Writes out supported prediction models.

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

type: integer

Number of nucleotides between previous and current variant across split.

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.

type: string
default: ${projectDir}/assets/external_tools_meta.json

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

type: string
default: linux

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

type: string
default: None

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

type: string
default: None

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

type: string
default: None

To use the ‘netmhcii’ tool, specify the path to the original software tarball for NetMHCII 2.2 here.

type: string
default: None

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

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

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|day)\s*)+$

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

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

Custom config file to supply to MultiQC.

hidden
type: string

Directory to keep pipeline Nextflow logs and reports.

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

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.

hidden
type: boolean