Options used by the germlinecnvcaller subworkflow

Specifies which analysis type for the pipeline- either ‘wgs’ or ‘wes’.

type: string

Length (in bp) of the bins. If zero, no binning will be performed.

type: number
default: 1000

Length (in bp) of the padding regions on each side of the intervals.

type: number

Name for panel of normals.

type: string
default: germlinecnvcaller

Output file format for count data

type: string

When scattering with this argument, each of the resultant files will (ideally) have this amount of interval-counts.

type: number
default: 5000

Options used by the gens subworkflow

Length (in bp) of the bins. If zero, no binning will be performed.

type: number
default: 100

Maximum chunk size when writing the HDF5 file

type: number
default: 167772150

Minimum interval median percentile for gatk CreateReadCountPanelOfNormals

type: number
default: 5

Name for panel of normals.

type: string
default: gens

Output file format for count data

type: string

Options used by the cnvkit subworkflow

Path to directory for target file.

type: string

Options used by the mutect2 subworkflow

Name for panel of normals.

type: string

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:

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

Most common options used for the pipeline

Tools to use for building Panel of Normals or models.

required
type: string

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

Path to FASTA genome file.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

Path to sequence dictionary file

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

Path to fasta index file

type: string
pattern: ^\S+\.fn?a(sta)?\.fai$

Path to GENS interval list file

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

Path to directory for a bed file containing regions to be exluded from the analysis.

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

Path to directory for exclude_interval_list file.

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

Path to Umap single-read mappability track in .bed or .bed.gz format. Overlapping intervals must be merged.

type: string

Path to a file containing ploidy priors table.

type: string

Path to segmental-duplication track in .bed or .bed.gz format. Overlapping intervals must be merged.

type: string

Path to directory for target bed file.

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

Path to directory for target interval_list file.

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

Path to target bed file

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

Do not load the iGenomes reference config.

hidden
type: boolean

The base path to the igenomes reference files

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

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

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/

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