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

Variants in VCF or TSV format.

required
type: string

Alleles as TXT file.

required
type: string

Peptide sequences in TSV format.

type: string

Protein sequences in FASTA format.

type: string

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})$

Options for the genome and proteome reference.

Specifies the human reference genome version.

type: string

Specifies the reference proteome.

type: string

Options for the reference genome indices used to align reads.

Directory / URL base for iGenomes references.

hidden
type: string
default: s3://ngi-igenomes/igenomes/

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 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

Specifies which memory mode should be used.

type: string
default: low

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

Workflow name.

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

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

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

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

hidden
type: string
default: 240.h

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 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