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

Other options specific to this pipeline.

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Workflow run mode.

type: string
pattern: ^(wgts|targeted)

Name of panel to use.

type: string

Skip check for restricted genome.

type: boolean

Skip check for known panels.

type: boolean

Run only processes manually provided in processes_include.

type: boolean

Pipeline processes to exclude.

type: string

Pipeline processes to include.

type: string

Prepare and write reference output only.

type: boolean

Create placeholders for reference data during stub run.

type: boolean

When positive, will use fastp to split fastq files so that each resultant fastq file has no more than max_fastq_records records. When nonpositive, fastp is not used and the provided fastq files are passed as-is to the aligner.

type: integer
default: 10000000

Enable fastp UMI processing.

type: boolean

fastp UMI location parameter (—umi_loc).

type: string

fastp UMI length parameter (—umi_len)

type: integer

fastp UMI skip parameter (—umi_skip)

type: integer
default: -1

Enable REDUX UMI processing.

type: boolean

UMI duplex delimiter as used by REDUX.

type: string

Path to GRIDSS configuration file.

type: string

User defined RNA read length used for Isofox.

type: integer

User defined Isofox expected GC ratios file.

type: string

User defined Isofox expected counts files (read length dependent).

type: string

User defined Isofox TPM normalisation file for panel data.

type: string

User defined Isofox gene list file for panel data.

type: string

Semicolon-separated list of Isofox functions to run

type: string
default: TRANSCRIPT_COUNTS;ALT_SPLICE_JUNCTIONS;FUSIONS;RETAINED_INTRONS

Reference data files and options required for the workflow.

Name of genome reference.

type: string

Version of reference genome.

hidden
type: string

Type of reference genome.

hidden
type: string

Do not load the iGenomes reference config.

hidden
type: boolean
default: true

The base path to the igenomes reference files

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

The base path to the HMF genome reference files

hidden
type: string
default: https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes

Path to HMF data.

type: string

Path to panel data.

type: string

Path to reference genome FASTA.

type: string

Path to reference genome FAI.

type: string

Path to reference genome dict.

type: string

Path to reference genome bwa-mem2 index.

type: string

Path to reference genome img.

type: string

Path to reference genome GRIDSS index.

type: string

Path to reference genome STAR index.

type: string

Path to reference genome GTF.

type: string

Path to HLA slice BED file.

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

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

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
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/oncoanalyser

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