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.

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: integer
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.

Directory for pre-built bwameme's learned 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

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 female panel of normals for Gens.

hidden
type: string

The female panel used to run DenoiseReadCounts.

Path to male panel of normals for Gens.

hidden
type: string

The male 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

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
default: chrM

Used to extract relevant information from the references to analyse mitochondria

File with mobile element references

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

Path to tsv file listing mobile element references.
Format: <mobile element type>\t<path to bed file>

File with mobile element allele frequency references

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

Path to csv file listing files containing mobile element allele frequencies in reference populations.
Format: <vcf file path>,<in_freq_info_key>,<in_allele_count_info_key>,<out_freq_info_key>,<out_allele_count_info_key>

Path to sentieon machine learning model file.

type: string

Path to mitochondrial FASTA genome file.

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

Path to a BED file containing PAR regions (used by deepvariant).

type: string
pattern: ^\S+\.bed(\.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. It needs to be the same as the intervals used to generate the ploidy and cnv models.

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

type: string

Vcf used for evaluating variant calls.

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

Path to comma-separated file containing information about the truth vcf files used by vcfeval.

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.

MT rank model config file for genmod.

type: string

SNV rank model config file for genmod.

type: string

SV rank model config file for genmod.

type: string

Directory for pre-built sdf index. Used by rtg/vcfeval

type: string

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

Path to the genome dictionary file

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

Databases used for structural variant annotation in chrA-posA-chrB-posB-type-count-frequency format.

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

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

Databases used for structural variant annotation in vcf format.

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

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

Should be Stranger's extended JSON as described at https://github.com/Clinical-Genomics/stranger/blob/master/stranger/resources/variant_catalog_grch37.json. This file is used by both ExpansionHunter and Stranger

Path to a file containing internal ids and customer ids in csv format.

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

Optional file to rename sample ids in the vcf2cytosure vcf

Path to vcf2cytosure blacklist file

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

Optional file to blacklist regions for VCF2cytosure

Path to a VCF file containing annotations.

type: string

Can be used to supply case-specific annotations in addition to those provided using --vcfanno_resources

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.

Databases used by both named and custom plugins to annotate variants.

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

Path to a file containing the absolute paths to databases and their indices used by VEP's custom and named plugins resources defined within the vcfanno toml file. One line per resource.

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

type: string

Path to a bed-like file exported by scout, which contains HGNC_IDs to be used in filter_vep.

type: string

Options used to steer the direction of the pipeline.

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

type: string

Specifies whether or not to use bwa as a fallback aligner in case bwamem2 throws an error.

type: boolean

errorStrategy needs to be set to ignore for the bwamem2 process for the fallback to work. Turned off by default.

Specifies the platform on which the reads were sequenced.

type: string
default: illumina

Method selection for ngs-bits samplegender

type: string

Specifies whether to run mitochondrial analysis for wes samples

type: boolean

Specifies whether to run rtgtools' vcfeval

type: boolean

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

type: boolean

Number of intervals to split your genome into (used to parallelize annotations)

type: integer
default: 20

Specifies whether or not to skip trimming with fastp.

type: boolean

Specifies whether or not to skip gens preprocessing subworkflow.

type: boolean

Specifies whether or not to skip CNV calling using GATK's GermlineCNVCaller

type: boolean

Specifies whether or not to skip peddy.

type: boolean

Specifies whether or not to skip calling mobile elements, and the subsequent annotation step.

type: boolean

Specifies whether or not to skip annotation of mobile elements.

type: boolean

Specifies whether or not to skip annotation of mitochondrial variants.

type: boolean

Specifies whether or not to subsample mt alignment.

type: boolean

Specifies whether or not to skip annotation of repeat expansions.

type: boolean

Specifies whether or not to skip calling of repeat expansions.

type: boolean

Specifies whether or not to skip smncopynumbercaller.

type: boolean

Specifies whether or not to skip annotate SNV subworkflow.

type: boolean

Specifies whether or not to skip nuclear and mitochondrial SNV calling and annotation.

type: boolean

Specifies whether or not to skip annotate structural variant subworkflow.

type: boolean

Specifies whether or not to skip nuclear and mitochondrial SV calling and annotation.

type: boolean

Specifies whether or not to skip the vcf2cytosure subworkflow

type: boolean
default: true

vcf2cytosure can generate CGH files from a structural variant VCF file that can be analysed in the CytoSure interpretation software. Cut-offs for allele frequencies and bin sizes can be modified in the config file. Turned off by default.

Specifies whether or not to filter results based on a list of candidate genes specified in 'vep_filters'.

type: boolean

Options to adjust parameters and filtering criteria for read alignments.

Specifies the alignment algorithm to use - available options are 'bwamem2', 'bwa', 'bwameme' and 'sentieon'.

type: string

Specifies the alignment algorithm to use - available options are 'bwamem2', 'bwa' and 'sentieon'.

type: string

Number of threads allocated for sorting alignment files (used only by bwameme)

type: integer
default: 4

To know more about this parameter check bwameme documentation.

Memory allocated for mbuffer in megabytes (used only by bwameme)

type: integer
default: 3072

To know more about this parameter check bwameme documentation.

Discard trimmed reads shorter than the given value

type: integer
default: 40

Minimum length of reads after adapter trimming. Shorter reads are discarded.

Expected coverage to subsample mt alignment to.

type: integer
default: 150

To know more about this parameter check samtools' view documentation.

Subsampling seed used to influence which subset of mitochondrial reads is kept.

type: integer
default: 30

To know more about this parameter check samtools' view documentation.

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

Bin size for CNVnator

type: integer
default: 1000

Option for selecting the PCR indel model used by Sentieon Dnascope.

type: string

PCR indel model used to weed out false positive indels more or less aggressively. The possible MODELs are: NONE (used for PCR free samples), and HOSTILE, AGGRESSIVE and CONSERVATIVE, in order of decreasing aggressiveness. The default value is CONSERVATIVE.

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.

File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs.

type: string

For more information check https://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html

File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SVs.

type: string

For more information check https://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html

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

type: integer
default: 112

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.

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

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