Variant callinglatest-release

longraredisease

nf-core/longraredisease

A Nextflow pipeline for rare disease diagnostics from Oxford Nanopore long-read sequencing data. Includes SV, SNV, CNV, and methylation profiling.

version1.0.0f40870fcbcJun 26, 2026 Upstream Usage docs

Key tools

FastQCMultiQC

Run it

nfclaw

nfclaw run longraredisease --input samplesheet.csv --outdir results --fasta-file <fasta_file> -profile docker

raw nextflow

nextflow run pipelines/longraredisease/upstream -profile docker --input samplesheet.csv --outdir results --fasta_file <fasta_file>

demo · bundled test profile

nfclaw run longraredisease --demo --outdir results   # adds the upstream test profile (-profile test,docker)

Inputs

column	type	required	allowed values	constraints
`sample`	string	yes		matches `^\S+$`
`file_path`	string	yes
`hpo_terms`	string	no		matches `^HP:\d{7}(;HP:\d{7})*$`
`sex`	integer	no	`1`, `2`, `0`
`phenotype`	integer	no	`1`, `2`, `0`, `-9`
`family_id`	string	no		matches `^\S+$`
`maternal_id`	string	no		matches `^\S+$`
`paternal_id`	string	no		matches `^\S+$`

--input must match ^\S+\.csv$.

The samplesheet is a CSV with this header (the columns the schema requires); fill each value per the table above and reference.md (no example value is invented here):

csv

sample,file_path

Any of the optional columns above may be appended to the header when your data needs them: hpo_terms, sex, phenotype, family_id, maternal_id, paternal_id.

From data files. --input may also be the data files — a directory (searched recursively), a quoted glob, or files (--input once per file) — from which nfclaw writes this samplesheet: sample from file names; file_path from files matching their patterns, by sample name. Optional columns left out take their schema defaults in the pipeline: sex = 0, phenotype = 0, family_id = unknown, maternal_id = 0, paternal_id = 0 — set them with --sheet-set where your design differs. Set other columns with --sheet-set COLUMN=VALUE. Preview it with --check; a run records it in <outdir>/provenance/ for replay.

Reference genome

No reference genome is set by default: supply your own reference. The schema declares AWS iGenomes at s3://ngi-igenomes/igenomes/; selecting --genome <id> uses the paths in the pipeline's reference configuration. Access to that remote source is required. To supply your own reference, use the reference_genome_options group in reference.md lists the reference options. Set --igenomes-ignore true to disable the lookup entirely. Confirm the selected reference's paths and source in the pinned upstream/nextflow.config and upstream/conf/ before running.

Resources

Resource requests follow the pipeline's configs and selected profiles. nf-core's resource labels often assume a server — a single step can request far more memory than a workstation has, and retry rules can increase requests. If a run fails with Process requirement exceeds available memory (or CPUs), cap every request, and every retry, at what this machine actually has:

bash

nfclaw run longraredisease --input samplesheet.csv --outdir results --fasta-file <fasta_file> -profile docker \
  --limit-cpus 4 --limit-memory 15.GB

nfclaw turns those into Nextflow's process.resourceLimits and passes them as a -c config — the mechanism nf-core prescribes for exactly this (docs). Set them to the machine's real capacity. --limit-time DURATION also caps how long any one task may run: a task that needs longer is stopped, and so is every retry, so set it only as a deliberate ceiling, never as a guess at how long the analysis takes. The generated config is kept in <outdir>/provenance/, so commands.sh replays the run under the same ceiling.

Nextflow engine

This release declares nextflowVersion = '!>=25.04.0'.

To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:

bash

nfclaw run longraredisease ... --nxf-ver 25.04.0

--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.

Demo

bash

nfclaw run longraredisease --demo --outdir results   # adds the upstream test profile (-profile test,docker)

Samplesheet

A CSV with this header (the columns the schema requires). Fill each value per the constraints below; optional columns from the table may be appended.

samplesheet.csv header

sample,file_path

Column	Type	Required	Allowed / constraints
`sample`	string	required	matches ^\S+$
`file_path`	string	required	—
`hpo_terms`	string	optional	matches ^HP:\d{7}(;HP:\d{7})*$
`sex`	integer	optional	`120`
`phenotype`	integer	optional	`120-9`
`family_id`	string	optional	matches ^\S+$
`maternal_id`	string	optional	matches ^\S+$
`paternal_id`	string	optional	matches ^\S+$

Required parameters

--inputstring (file path)

Path to comma-separated file containing information about the samples in the experiment.

Constraint · matches ^\S+\.csv$

--fasta-filestring (file path)

Path to FASTA genome file.

Constraint · matches ^\S+\.fn?a(sta)?(\.gz)?$

Parameter explorer

96 parameters · 11 groups

Every parameter from the pinned nextflow_schema.json. nfclaw checks explicit values before launch; complex rules use the pinned pipeline's runtime validation. Search, filter by group, and expand any parameter for its default, allowed values and constraints.

Groups

nextflow_schema.json

71 parameters · 25 hidden

Cnv Calling options6

Path to BED file for regions to exclude in HiFiCNV.

BED file with expected CNVs for HiFiCNV evaluation.

Spectre bin size

Path to Spectre blacklist BED file.

Path to Spectre metadata file.

Use test data for Spectre CNV calling.

Generic options4

Display the help message.

Display the full detailed help message.

Custom MultiQC yaml file containing HTML including a methods description.

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

Input Output options3

Email address for completion summary.

Path to comma-separated file containing information about the samples in the experiment.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Output options2

Generate SNF output.

Generate VCF output.

Reference Genome options4

List of chromosome codes to process.

Path to FASTA genome file.

Name of iGenomes reference.

Path to tandem repeat BED file for Sniffles.

Snv Calling options10

Enable structural variant annotation.

Minimum mapping quality for Clair3 to consider an alignment.

Clair3 model to use.

Clair3 platform.

Extra arguments for DeepVariant make_examples step.

BED file with regions to restrict DeepVariant calling to.

Enable generation of a runtime report for DeepVariant.

Filter PASS variants only in SNV.

Run DeepVariant, otherwise runs Clair3.

SnpEff database to use for annotation

Str Analysis options3

Path to STR BED file.

Path to variant catalogue JSON file.

Sv Annotation options3

Output format for SvAnna results.

Enable SV annotation with SvAnna.

Path to the SvAnna database directory.

Sv Calling options15

Enable structural variant annotation.

Path to AnnotSV annotations directory.

BED file with coverage information for SV filtering.

Minimum mapping quality for cuteSV.

Enable SV filtering by coverage.

Only consider PASS variants.

Merge SV calls from multiple callers.

This is set for jasmine - minimum number of callers supporting the variant

Minimum read support for SVs.

Minimum read support limit.

Rank filtering criteria

Set off variant caller - SVIM

Minimum mapping quality for Sniffles.

Minimum mapping quality for SVIM.

Workflow options21

Enable annotation of unified VCF

Enable CNV calling with HiFiCNV if cnv_spectre is false.

Enable filtering of alignments to target regions.

Generate BAM statistics using samtools.

Generate coverage statistics.

Enable haplotagging of BAM files.

Input file type.

Enable methylation calling.

Minimap2 model for alignment.

Enable modification of STR calls

Enable quality control analysis.

Sequencing platform (e.g. 'ont', 'hifi', 'pacbio').

Enable single nucleotide variant calling.

Enable short tandem repeat analysis.

Enable structural variant calling.

BED file with target regions for filtering.

Enable trio analysis for SNV calling and phasing.

Enable VCF unification

Use Winnowmap for alignment instead of Minimap2

Path to repetitive k-mer file for Winnowmap

Winnowmap model for alignment.

Outputs

Results land in --outdir; the files and directory layout depend on the selected workflow, parameters and publication settings. Run metadata is normally placed in <outdir>/pipeline_info/ (execution report, software versions), when those outputs are enabled. The pinned tree includes MultiQC support; a report is produced only when its workflow step runs. nfclaw run also writes <outdir>/provenance/ with the exact params file and the run log, <outdir>/provenance/logs/run.log — the whole launch, whose last line states the outcome (Nextflow's own log is <outdir>/.nextflow.log); unless --no-provenance it adds a run manifest (pinned version, commit and exact command), input/output SHA-256 checksums, and a replayable commands.sh. The exact output files and directory layout for this release are documented upstream: github.com/nf-core/longraredisease/blob/1.0.0/docs/output.md Check a run — in the foreground or the background — with nfclaw status <outdir>: success, still running, how it ended (with the error), or stopped without an outcome; exit 0 success, 3 running, 1 otherwise.