Define where the pipeline should find input data and save output data.

Path to the samplesheet file containing information about the samples in the experiment.

type: string
pattern: ^\S+\.(csv|tsv|json|yaml|yml)$

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

Directory for pre-built bwa index.

type: string

Directory for pre-built bwamem2 index.

type: string

Directory for pre-built bwameme’s learned 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

Path to a list of common SNP locations for Gens.

hidden
type: string

Path to interval list for Gens.

hidden
type: string

Path to female panel of normals for Gens.

hidden
type: string

Path to male 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$

The base path to the igenomes reference files

hidden
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
default: chrM

File with mobile element references

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

File with mobile element allele frequency references

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

Base path / URL for data used in the modules

hidden
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)?$

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

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

Vcf used for evaluating variant calls.

type: string
pattern: ^\S+\.(csv|tsv|json|yaml|yml)$

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

type: boolean

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

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|tsv|json|yaml|yml)$

Databases used for structural variant annotation in vcf format.

type: string
pattern: ^\S+\.(csv|tsv|json|yaml|yml)$

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 internal ids and customer ids in csv format.

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

Path to a BED file containing markers used by verifybamid2.

type: string

Path to mean matrix file of genotype matrix. Used by verifybamid2.

type: string

Path to UD matrix file from SVD result of genotype matrix. Used by verifybamid2.

type: string

Path to vcf2cytosure blacklist file

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

Path to a VCF file containing annotations.

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

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

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

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

Specifies whether to generate a concatenated VCF file containing both nuclear & mitochondrial snv calls

type: boolean

After aligning the reads to a reference, extract alignments from specific regions/contigs and restrict the analysis to those regions/contigs.

type: boolean
default: false

Specifies the platform on which the reads were sequenced.

type: string
default: illumina

Method selection for ngs-bits samplegender

type: string

Can be specified as RNAME[:STARTPOS]. Multiple regions should be seperated by space

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

Disable specified subworkflows.

type: string

Disable specified tools.

type: string

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

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

type: integer
default: 3072

Discard trimmed reads shorter than the given value

type: integer
default: 40

Expected coverage to subsample mt alignment to.

type: integer
default: 150

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

type: integer
default: 30

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. Used only by sentieon.

type: string

Bin size for CNVnator

type: integer
default: 1000

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

type: string

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

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

type: string

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

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.

hidden
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