Introduction Usage Parameters Output Results Releases

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})$

Options to configure the workflow execution mode.

Input file type.

type: string

Sequencing platform (e.g. ‘ont’, ‘hifi’, ‘pacbio’).

type: string
default: ont

Minimap2 model for alignment.

type: string

Use Winnowmap for alignment instead of Minimap2

type: boolean

Winnowmap model for alignment.

type: string

Path to repetitive k-mer file for Winnowmap

type: string

Enable haplotagging of BAM files.

type: boolean
default: true

Enable trio analysis for SNV calling and phasing.

type: boolean
default: true

Enable filtering of alignments to target regions.

type: boolean

BED file with target regions for filtering.

type: string

Generate BAM statistics using samtools.

type: boolean
default: true

Generate coverage statistics.

type: boolean
default: true

Enable structural variant calling.

type: boolean
default: true

Enable single nucleotide variant calling.

type: boolean
default: true

Enable CNV calling with HiFiCNV if cnv_spectre is false.

type: boolean

Enable short tandem repeat analysis.

type: boolean
default: true

Enable quality control analysis.

type: boolean
default: true

Enable methylation calling.

type: boolean
default: true

Reference genome related files and options required for the workflow.

Path to FASTA genome file.

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

Path to BED file for coverage analysis (optional).

type: string

Path to tandem repeat BED file for Sniffles.

type: string

List of chromosome codes to process.

type: array

Options for structural variant calling and filtering.

Minimum mapping quality for Sniffles.

type: integer
default: 10

Enable structural variant annotation.

type: boolean
default: true

Merge SV calls from multiple callers.

type: boolean
default: true

Minimum mapping quality for SVIM.

type: integer
default: 10

Minimum mapping quality for cuteSV.

type: integer
default: 10

Only consider PASS variants.

type: boolean
default: true

Enable SV filtering by coverage.

type: boolean
default: true

BED file with coverage information for SV filtering.

type: string

Minimum read support for SVs.

type: string
default: auto

Minimum read support limit.

type: integer
default: 2

Path to AnnotSV annotations directory.

type: string

Options for SV annotation and prioritization with SvAnna.

Enable SV annotation with SvAnna.

type: boolean

Path to the SvAnna database directory.

type: string

Output format for SvAnna results.

type: string

Options for single nucleotide variant calling.

Run DeepVariant, otherwise runs Clair3.

type: boolean
default: true

Filter PASS variants only in SNV.

type: boolean
default: true

Minimum mapping quality for Clair3 to consider an alignment.

type: integer
default: 10

Clair3 model to use.

type: string
default: ont

Clair3 platform.

type: string
default: ont

BED file with regions to restrict DeepVariant calling to.

type: string

Enable generation of a runtime report for DeepVariant.

type: boolean
default: true

Extra arguments for DeepVariant make_examples step.

type: string
default: min_mapping_quality=10

Options for copy number variant calling.

Path to BED file for regions to exclude in HiFiCNV.

type: string

BED file with expected CNVs for HiFiCNV evaluation.

type: string

Use test data for Spectre CNV calling.

type: boolean

Path to Spectre metadata file.

type: string

Path to Spectre blacklist BED file.

type: string

Path to test summary file for Spectre CNV calling.

hidden
type: string

Path to test regions BED file for Spectre CNV calling.

hidden
type: string

Path to test regions CSI file for Spectre CNV calling.

hidden
type: string

Path to test FASTA file for Spectre CNV calling.

hidden
type: string

Path to test Clair3 VCF for Spectre CNV calling.

hidden
type: string

Options for short tandem repeat analysis.

Path to STR BED file.

type: string

Path to variant catalogue JSON file.

type: string

Options for output formats.

Generate VCF output.

type: boolean
default: true

Generate SNF output.

type: boolean
default: true

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

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

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

Show full help message.

hidden
type: boolean

Show hidden parameters.

hidden
type: boolean
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