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$

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.

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})$

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

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

If none provided, will be generated automatically from the FASTA reference.

Directory for pre-built bwamem2 index.

type: string

If none provided, will be generated automatically from the FASTA reference.

Path to the directory containing cadd annotations.

type: string

This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.

Path to FASTA genome index file.

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

If none provided, will be generated automatically from the FASTA reference

Path to FASTA genome file.

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

This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.

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

type: string

This model is required for generating a cnv calls when using GermlineCNVCaller.

Name of iGenomes reference.

type: string
default: GRCh38

If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.

See the nf-core website docs for more details.

Path to a list of common SNP locations for Gens.

hidden
type: string

Locations of gnomad SNPs with a high enough BAF.

Path to interval list for Gens.

hidden
type: string

This file contains the binning intervals used for CollectReadCounts.

Path to panel of normals for Gens.

hidden
type: string

The panel used to run DenoiseReadCounts.

Path to the gnomad tab file with allele frequencies.

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

Path to the gnomad tab file with CHR/START/REF,ALT/AF. Can be generated from the gnomad annotations vcf.

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

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

Path to the index of gnomad tab file with CHR/START/REF,ALT/AF

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

type: boolean

Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.

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 genome. This is used to calculate genome-wide coverage statistics.

Path to the interval list of the Y chromosome.

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

Path to the interval list of the Y chromosome. This is used to calculate coverage statistics for the Y chromosome.

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

This folder is a flat structure with file names that map to the config.

Name of the mitochondrial contig in the reference fasta file

type: string

Used to extract relevant information from the references to analyse mitochondria

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

Produced in GATK4 DetermineGermlineContigPloidy cohort, this model is required for generating a cnv model when using GermlineCNVCaller.

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

type: string

Generated by GATK4 preprocessintervals. If absent, pipeline can generate this file.

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

The saved references can be used for future pipeline runs, reducing processing times.

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 comma-separated file containing information about the databases used for structural variant annotation.

Path to directory for target bed file.

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

If you would like to limit your analysis to specific regions of the genome, you can pass those regions in a bed file using this option

Path to variant catalog file

type: string

Used with ExpansionHunter and if no catalogue is passed, then a default will be used.

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

type: string

If no file is passed, default configurations will be used according to genome build within the context of the pipeline.

Path to the vcfanno toml file.

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

If no toml is passed, default configurations will be used according to genome build within the context of the pipeline.

Path to the vcfanno lua file.

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

Custom operations file (lua). For use when the built-in ops don't supply the needed reduction.

Path to vep's cache directory.

type: string

If no directory path is passed, vcf files will not be annotated by vep.

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

If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.

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

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

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$

Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'

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*)+$

Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'

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

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

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})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

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

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

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

By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

By default, when an unrecognised parameter is found, it returns a warinig.

Validation of parameters in lenient more.

hidden
type: boolean

Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.