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|tsv|yaml|yml|json)$

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

Sample id

type: string

The analysis type used by the input files

type: string

The benchmarking methods to use. Should be a comma-separate list of one or more of the following options: truvari, svanalyzer, happy, sompy, rtgtools, wittyer

type: string

SMALL: Path to the high confidence BED or VCF files.

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

SMALL: High confidence BED files

SMALL: Path to the golden set VCF files.

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

SMALL: Truth or golden set VCF file, to be used for comparisons

SNVs: Path to the high confidence BED or VCF files.

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

SNVs: High confidence BED files

SNVs: Path to the golden set VCF files.

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

SNVs: Truth or golden set VCF file, to be used for comparisons

INDELs: Path to the high confidence BED or VCF files.

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

INDELs: High confidence BED files

INDELs: Path to the golden set VCF files.

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

INDELs: Truth or golden set VCF file, to be used for comparisons

SV: Path to the high confidence BED or VCF files.

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

SV: High confidence BED files

SV: Path to the golden set VCF files.

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

SV: Truth or golden set VCF file, to be used for comparisons

CNV: Path to the high confidence BED or VCF files.

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

CNV: High confidence BED files

CNV: Path to the golden set VCF files.

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

CNV: Truth or golden set VCF file, to be used for comparisons

The preprocessing steps to perform on the input files. Should be a comma-separated list of one or more of the following options: normalization, deduplication, prepy, filter_contigs

type: string

The standardization methods to perform on the input files. Should be a comma-separated list of one or more of the following options: homogenize, svync

type: string

Minimum SV size of variants to benchmark, 0 to disable , Default:30

type: integer

Maximum SV size of variants to benchmark, -1 to disable , Default:-1

type: integer

Minimum Alele Frequency of variants to benchmark, Use -1 to disable , Default:-1

type: number

Minimum number of read supporting variants to benchmark, Use, -1 to disable , Default:-1

type: integer

Use bcftools expressions https://samtools.github.io/bcftools/bcftools.html#expressions to exclude variants. Default:null

type: string

Use bcftools expressions https://samtools.github.io/bcftools/bcftools.html#expressions to include variants. Default:null

type: string

Email address for completion summary.

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.

type: string

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

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 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.

Path to FAI genome file.

required
type: string

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.

The SDF file needed to run rtgtools vcfeval

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

This will be automatically generated by the pipeline when missing

Do not load the iGenomes reference config.

hidden
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.

Do not load the truth reference config.

hidden
type: boolean

Do not load truth.config when running the pipeline. In this case user need to provide necessary truth files. You may choose this option if you observe clashes between custom parameters and those supplied in truth.config.

Run liftover workflow

hidden
type: boolean

Makes the use of liftover subworkflow, hg37 truth sets will liftover to hg38 and visa versa. Has to be either combined with itruth.config or --chain and --rename_chr.

Path to the chain file sey required for liftover.

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

This parameter is mandatory if --liftover is true and --genome is not specified and --itruth is false. A chain can be found under itruth files and can be used together with --genome.

Path to the ranaming chromosomes for lifting over.

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

This parameter is mandatory if --liftover is true and --genome is not specified and --itruth is false. A rename can be found under assets/rename_contigs or can be used together with --genome.

The dictionary file is required ofr liftover process. It has to be .dict of genome file used in the workflow.

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

This will be automatically generated by the pipeline when missing

Parameters used to describe centralized 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

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.

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.

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/