variantprioritization
nf-core/variantprioritization
pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number abberations for precision cancer medicine
Key tools
Run it
nfclaw run variantprioritization --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/variantprioritization/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run variantprioritization --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
patient | string | yes | matches ^\S+$ | |
status | integer | yes | 0, 1 | |
sample | string | yes | matches ^\S+$ | |
vcf | string (file path) | yes | matches ^\S+\.vcf(\.gz)?$ | |
cna | string (file path) | no | matches ^\S+\.(cns|txt)$ |
--input must match ^\S+\.csv$.
The samplesheet is a CSV with this header (the columns the schema requires); fill each value per the table above and reference.md (no example value is invented here):
patient,status,sample,vcfAny of the optional columns above may be appended to the header when your data needs them: cna.
From data files. --input may also be the data files — a directory (searched recursively), a quoted glob, or files (--input once per file) — from which nfclaw writes this samplesheet: sample from file names; vcf, cna from files matching their patterns, by sample name. Set the required columns no file determines with --sheet-set COLUMN=VALUE (a constant or a {sample}/{lane} template): patient (matching ^\S+$); status (one of 0, 1). 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_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:
nfclaw run variantprioritization --input samplesheet.csv --outdir results -profile docker \ --limit-cpus 4 --limit-memory 15.GBnfclaw 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 = '!>=25.10.0'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run variantprioritization ... --nxf-ver 25.10.0--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run variantprioritization --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.
patient,status,sample,vcf| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
patient | string | required | matches ^\S+$ |
status | integer | required | 01 |
sample | string | required | matches ^\S+$ |
vcf | string (file path) | required | matches ^\S+\.vcf(\.gz)?$ |
cna | string (file path) | optional | matches ^\S+\.(cns|txt)$ |
Required parameters
--inputstring (file path)Path to comma-separated file containing information about the samples in the experiment.
Constraint · matches ^\S+\.csv$
--outdirstring (directory path)The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Parameter explorer
111 parameters · 9 groupsEvery 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.
89 parameters · 22 hidden
Cpsr options13
Also provide CPSR TIER classifications for variants with existing ClinVar classifications.
Include ClinVar variants linked to non-cancer phenotypes/conditions.
Path to custom gene list file (single-column Ensembl gene identifiers).
Display name for custom panel/list.
For PanelApp panels (1-44), include GREEN-status genes only.
Report overlap with low/moderate-risk GWAS cancer variants.
Ignore non-coding (non protein-altering) variants in CPSR report.
Upper gnomAD global MAF threshold for variants included in report.
Comma-separated CPSR virtual panel identifier(s).
Report overlap with pharmacogenomic toxicity variants (CPIC/PgX).
gnomAD population source used for ACMG frequency assessment.
Include variants in ACMG secondary findings gene list (v3.2).
Consider basic GENCODE transcript set only with Variant Effect Predictor (VEP) (option '--gencode_basic' in VEP).
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 options4
Email address for completion summary.
Path to comma-separated file containing information about the samples in the experiment.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Pcgr options33
Use all reference SBS signatures during signature re-fitting.
Type of DNA sequencing assay performed for input data.
VCF INFO tag for somatic call confidence.
Enable copy-number alteration (CNA) analysis and reporting.
Mean percent overlap between CNA segment and gene transcripts for reporting gains/losses.
Maximum control/normal allelic depth (ALT-supporting reads) allowed when control depth+AF tags are provided.
Maximum control/normal allelic fraction allowed when control AF tag is provided.
VCF INFO tag for control/normal variant allelic fraction.
Minimum control/normal depth for variant inclusion when control depth tag is provided.
VCF INFO tag for control/normal sequencing depth.
Effective target size in Mb for TMB calculation.
Predict microsatellite instability (MSI) status.
Estimate mutational signature contributions by re-fitting.
Estimate tumor mutational burden (TMB).
Include sequencing artefact signatures during fitting.
Path to CPSR-classified germline calls file.
Path to CPSR YAML configuration file.
Minimum number of SNVs required for mutational signature re-fitting.
Do not generate PCGR HTML report.
Minimum tumor-type prevalence (%) of reference signatures to include in re-fitting.
Minimum tumor allelic depth (ALT-supporting reads) required for TMB calculation when depth+AF tags are available.
Minimum tumor allelic fraction required for inclusion in TMB calculation when AF tag is available.
TMB measure to show in report.
Minimum tumor depth required for inclusion in TMB calculation when depth tag is available.
Minimum tumor allelic depth (ALT-supporting reads) for variant inclusion when tumor depth+AF tags are provided.
Minimum tumor allelic fraction for variant inclusion when tumor AF tag is provided.
VCF INFO tag for tumor variant allelic fraction.
Minimum tumor depth for variant inclusion when tumor depth tag is provided.
VCF INFO tag for tumor sequencing depth.
Estimated tumor ploidy.
Estimated tumor purity.
Primary tumor type/site code used for site-specific interpretation.
Generate a MAF file for the input VCF using vcf2maf.
Pcgr Tumoronly options16
Exclude variants with dbSNP support for non-somatic origin.
Exclude variants likely to represent heterozygous germline events.
Exclude variants likely to represent homozygous germline events.
Exclude non-exonic variants in tumor-only filtering.
Exclude variants overlapping panel-of-normals calls.
Maximum gnomAD AFR population AF tolerated in tumor-only filtering.
Maximum gnomAD AMR population AF tolerated in tumor-only filtering.
Maximum gnomAD ASJ population AF tolerated in tumor-only filtering.
Maximum gnomAD EAS population AF tolerated in tumor-only filtering.
Maximum gnomAD FIN population AF tolerated in tumor-only filtering.
Maximum global gnomAD AF tolerated in tumor-only filtering.
Maximum gnomAD NFE population AF tolerated in tumor-only filtering.
Maximum gnomAD OTH population AF tolerated in tumor-only filtering.
Maximum gnomAD SAS population AF tolerated in tumor-only filtering.
Path to panel-of-normals (PoN) VCF used to suppress recurrent artefacts.
Run in tumor-only mode (no matched normal sample).
Reference options6
Name of iGenomes reference.
PCGR/CPSR reference data bundle version.
Path to PCGR database. Set pcgr_download to false when using this.
Download PCGR reference database from the PCGR site. Set to false if you want to use a local path.
Path to VEP cache.
VEP cache version.
Variantfiltering options8
Filtering expression for DeepVariant VCF records.
Filtering expression for FreeBayes germline VCF records.
Filtering expression for FreeBayes somatic VCF records.
Filtering expression for HaplotypeCaller VCF records.
Filtering expression for Mutect2 VCF records.
Filtering expression for Strelka INDEL records.
Filtering expression for Strelka SNV records.
Filtering expression for combined Strelka variant records.
Vep Params options5
Number of variants buffered per VEP processing block.
Use full GENCODE transcript set during annotation.
Number of parallel VEP forks.
Skip annotation of intergenic variants.
Priority order used by VEP when selecting a single representative consequence.
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/variantprioritization/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.