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.

hidden
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.

hidden
type: string

Reference genome related files and options required for the workflow.

The amount to pad each end of the target intervals to create bait intervals.

type: number
default: 100
pattern: ^\S+\.bed(\.gz)?$

Directory for pre-built bwa index.

type: string

Directory for pre-built bwamem2 index.

type: string

Path to the directory containing cadd annotations.

type: string

Path to FASTA genome index file.

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

Path to FASTA genome file.

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

A file containing the path to models produced by GATK4 GermlineCNVCaller cohort.

type: string

Name of iGenomes reference.

type: string
default: GRCh38

Path to a list of common SNP locations for Gens.

hidden
type: string

Path to interval list for Gens.

hidden
type: string

Path to panel of normals for Gens.

hidden
type: string

Path to the gnomad tab file with allele frequencies.

type: string
pattern: ^\S+\.tab(\.gz)?$

Path to the index file for the gnomad tab file with allele frequencies.

type: string
pattern: ^\S+\.bed(\.gz)?\.idx$

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

type: boolean

Path to the interval list of the genome (autosomes, sex chromosomes, and mitochondria).

required
type: string
pattern: ^\S+\.intervals?(_list)?$

Path to the interval list of the Y chromosome.

required
type: string
pattern: ^\S+\.intervals?(_list)?$

Path to known dbSNP file.

type: string
pattern: ^\S+\.vcf(\.gz)?$

Path to known dbSNP file index.

type: string
pattern: ^\S+\.vcf(\.gz)?\.tbi$

Local directory base for genome references that map to the config.

type: string

Name of the mitochondrial contig in the reference fasta file

type: string

Path to sentieon machine learning model file.

type: string

Path to mitochondrial FASTA genome file.

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

Directory containing the ploidy model files

type: string

Interval list file containing the intervals over which read counts are tabulated for CNV calling

type: string

File with gene ids that have reduced penetrance. For use with genmod

type: string

If generated by the pipeline save the required indices/references in the results directory.

type: boolean

SNV rank model config file for genmod.

type: string

SV rank model config file for genmod.

type: string

Path to the genome dictionary file

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

Databases used for structural variant annotation.

type: string

Path to directory for target bed file.

type: string
pattern: ^\S+\.bed(\.gz)?$

Path to variant catalog file

type: string

Path to a file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource.

type: string

Path to the vcfanno toml file.

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

Path to the vcfanno lua file.

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

Path to vep’s cache directory.

type: string

Path to the file containing HGNC_IDs of interest on separate lines.

type: string

Options used to steer the direction of the pipeline.

Specifies which analysis type for the pipeline- either ‘wgs’,‘wes’,‘mito’. This changes resources consumed and tools used.

type: string

Specifies whether or not to run gens preprocessing subworkflow.

type: boolean

Specifies which analysis type for the pipeline- either ‘wgs’,‘wes’,‘mito’. This changes resources consumed and tools used.

type: string

Specifies whether to generate and publish alignment files as cram instead of bam

type: boolean

Specifies whether or not to skip CNV calling.

type: boolean

Specifies whether or not to skip the subworkflow that analyses mitochondrial genome separate from the nuclear genome.

type: boolean

Specifies whether or not to skip annotate SNV subworkflow.

type: boolean

Specifies whether or not to skip annotate structural variant subworkflow.

type: boolean

Options to adjust parameters and filtering criteria for read alignments.

Specifies the alignment algorithm to use - available options are ‘bwamem2’ and ‘sentieon’.

type: string

Specifies whether duplicates reads should be removed prior to variant calling.

type: boolean

Options to adjust parameters and filtering criteria for variant calling.

Interval in the reference that will be used in the software

type: string

Indicates whether the sample library is amplified using PCR or not. Set to false for PCR Free samples.

type: boolean

Specifies the variant caller to use - available options are ‘deepvariant’ and ‘sentieon’.

type: string

Specifies the variant types for sentieon variant caller.

type: string

Options used to facilitate the annotation of the variants.

Specify the version of the VEP cache provided to the --vep_cache option.

type: integer

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|d|day)\s*)+$

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

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.

hidden
type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean