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$

Path to 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})$

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

MHC class for prediction.

type: integer

Specifies the maximum peptide length.

type: integer
default: 11

Specifies the minimum peptide length.

type: integer
default: 8

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 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.

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.

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

type: string
default: None

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

type: string
default: None

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

type: string
default: None

To use the ‘netmhcii’ tool, specify the path to the original software tarball for NetMHCII 2.2 (Linux) 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

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