Introduction Usage Parameters Output

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.

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.

type: string

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

Do not load the iGenomes reference config.

hidden
type: boolean

The base path to the igenomes reference files

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

PCGR/CPSR reference data bundle version.

type: integer
default: 20250314

Path to PCGR database. Set pcgr_download to false when using this.

type: string

Download PCGR reference database from the PCGR site. Set to false if you want to use a local path.

type: boolean
default: true

Path to VEP cache.

type: string
default: s3://annotation-cache/vep_cache/

VEP cache version.

type: integer
default: 113

VEP species. Defaults to homo_sapiens.

hidden
type: string
default: homo_sapiens

Configuration options for germline cancer predisposition reporting (CPSR).

Comma-separated CPSR virtual panel identifier(s).

type: string
default: 0
pattern: ^\d+(,\d+)*$

Path to custom gene list file (single-column Ensembl gene identifiers).

type: string

Display name for custom panel/list.

type: string

For PanelApp panels (1-44), include GREEN-status genes only.

type: boolean

Include variants in ACMG secondary findings gene list (v3.2).

type: boolean

Report overlap with pharmacogenomic toxicity variants (CPIC/PgX).

type: boolean

Report overlap with low/moderate-risk GWAS cancer variants.

type: boolean

gnomAD population source used for ACMG frequency assessment.

type: string

Upper gnomAD global MAF threshold for variants included in report.

type: number
default: 0.9

Also provide CPSR TIER classifications for variants with existing ClinVar classifications.

type: boolean

Include ClinVar variants linked to non-cancer phenotypes/conditions.

type: boolean

Ignore non-coding (non protein-altering) variants in CPSR report.

type: boolean

Configuration options for somatic interpretation and reporting with PCGR.

Generate a MAF file for the input VCF using vcf2maf.

type: boolean

Type of DNA sequencing assay performed for input data.

type: string

Primary tumor type/site code used for site-specific interpretation.

type: integer

Estimated tumor ploidy.

type: string

Enable copy-number alteration (CNA) analysis and reporting.

type: boolean

Mean percent overlap between CNA segment and gene transcripts for reporting gains/losses.

type: integer
default: 50

VCF INFO tag for tumor sequencing depth.

type: string

VCF INFO tag for tumor variant allelic fraction.

type: string

VCF INFO tag for control/normal sequencing depth.

type: string

VCF INFO tag for control/normal variant allelic fraction.

type: string

VCF INFO tag for somatic call confidence.

type: string

Estimated tumor purity.

type:

Effective target size in Mb for TMB calculation.

type: integer
default: 34

Path to CPSR-classified germline calls file.

type: string

Path to CPSR YAML configuration file.

type: string

Estimate tumor mutational burden (TMB).

type: boolean

Predict microsatellite instability (MSI) status.

type: boolean

Estimate mutational signature contributions by re-fitting.

type: boolean

TMB measure to show in report.

type: string

Minimum tumor depth required for inclusion in TMB calculation when depth tag is available.

type: integer

Minimum tumor allelic fraction required for inclusion in TMB calculation when AF tag is available.

type: number

Minimum tumor allelic depth (ALT-supporting reads) required for TMB calculation when depth+AF tags are available.

type: integer

Minimum number of SNVs required for mutational signature re-fitting.

type: integer
default: 200

Use all reference SBS signatures during signature re-fitting.

type: boolean

Include sequencing artefact signatures during fitting.

type: boolean

Minimum tumor-type prevalence (%) of reference signatures to include in re-fitting.

type: number
default: 0.1

Minimum tumor depth for variant inclusion when tumor depth tag is provided.

type: integer

Minimum tumor allelic depth (ALT-supporting reads) for variant inclusion when tumor depth+AF tags are provided.

type: integer

Minimum tumor allelic fraction for variant inclusion when tumor AF tag is provided.

type: integer

Minimum control/normal depth for variant inclusion when control depth tag is provided.

type: integer

Maximum control/normal allelic depth (ALT-supporting reads) allowed when control depth+AF tags are provided.

type: integer

Maximum control/normal allelic fraction allowed when control AF tag is provided.

type: integer
default: 1

Do not generate PCGR HTML report.

type: boolean

Additional filtering options for tumor-only somatic interpretation.

Run in tumor-only mode (no matched normal sample).

type: boolean

Path to panel-of-normals (PoN) VCF used to suppress recurrent artefacts.

type: string

Exclude variants overlapping panel-of-normals calls.

type: boolean

Exclude variants likely to represent homozygous germline events.

type: boolean

Exclude variants likely to represent heterozygous germline events.

type: boolean

Exclude variants with dbSNP support for non-somatic origin.

type: boolean

Exclude non-exonic variants in tumor-only filtering.

type: boolean

Maximum gnomAD NFE population AF tolerated in tumor-only filtering.

type: number
default: 0.002

Maximum gnomAD FIN population AF tolerated in tumor-only filtering.

type: number
default: 0.002

Maximum gnomAD ASJ population AF tolerated in tumor-only filtering.

type: number
default: 0.002

Maximum gnomAD OTH population AF tolerated in tumor-only filtering.

type: number
default: 0.002

Maximum gnomAD AMR population AF tolerated in tumor-only filtering.

type: number
default: 0.002

Maximum gnomAD AFR population AF tolerated in tumor-only filtering.

type: number
default: 0.002

Maximum gnomAD EAS population AF tolerated in tumor-only filtering.

type: number
default: 0.002

Maximum gnomAD SAS population AF tolerated in tumor-only filtering.

type: number
default: 0.002

Maximum global gnomAD AF tolerated in tumor-only filtering.

type: number
default: 0.002

Custom expressions for caller-specific hard filtering.

Filtering expression for HaplotypeCaller VCF records.

type: string
default: -i\'FORMAT/DP>10\

Filtering expression for DeepVariant VCF records.

type: string
default: -i\'FORMAT/DP>10\

Filtering expression for combined Strelka variant records.

type: string
default: -i\'FORMAT/DP>10\

Filtering expression for FreeBayes germline VCF records.

type: string
default: -i\'FORMAT/DP>10\

Filtering expression for Mutect2 VCF records.

type: string
default: -i\'FORMAT/DP>10\

Filtering expression for FreeBayes somatic VCF records.

type: string
default: -i\'FORMAT/DP>10\

Filtering expression for Strelka INDEL records.

type: string
default: -i\'FORMAT/DP>10\

Filtering expression for Strelka SNV records.

type: string
default: -i\'FORMAT/DP>10\

Runtime and annotation behavior options for Ensembl VEP.

Number of parallel VEP forks.

type: integer
default: 4

Number of variants buffered per VEP processing block.

type: integer
default: 500

Use full GENCODE transcript set during annotation.

type: boolean
default: true

Priority order used by VEP when selecting a single representative consequence.

type: string
default: mane_select,mane_plus_clinical,canonical,biotype,ccds,rank,tsl,appris,length

Skip annotation of intergenic variants.

type: boolean

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.

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

Display the help message.

type: boolean,string

Display the full detailed help message.

type: boolean

Display hidden parameters in the help message (only works when —help or —help_full are provided).

type: boolean
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