pacvar
nf-core/pacvar
A variant caller for PacBio long read sequencing - also can be used for PureTarget panel analysis, and quantification of repeat expansions
Key tools
Run it
nfclaw run pacvar --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/pacvar/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run pacvar --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
sample | string or integer | yes | matches ^\S+$ | |
bam | string (file path) | yes | matches ^\S+\.(bam|cram)$ | |
pbi | string (file path) | no | matches ^\S+\.(bai|crai|pbi)$ | |
fail | string (file path) | no | matches ^\S+\.(bam|cram)$ | |
repeat_id | string | no | ||
karyotype | string | no | XX, XY |
--input must match ^\S+\.(csv|tsv|json|yaml|yml)$.
For tabular CSV/TSV input, use this header (the columns the schema requires); fill each value per the table above and reference.md (no example value is invented here):
sample,bamAny of the optional columns above may be appended to the header when your data needs them: pbi, fail, repeat_id, karyotype.
From data files. --input may also be the data files — a directory (searched recursively), a quoted glob, or files (--input once per file) — from which nfclaw writes this samplesheet: sample from file names; pbi from files matching their patterns, by sample name. Set the required columns no file determines with --sheet-set COLUMN=VALUE (a constant or a {sample}/{lane} template): bam (matching ^\S+.(bam|cram)$). 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 e.g. --fasta; the reference_genome_options group in reference.md lists every reference option. 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 pacvar --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 = '!>=25.10.4'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run pacvar ... --nxf-ver 25.10.4--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run pacvar --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.
sample,bam| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
sample | string or integer | required | matches ^\S+$ |
bam | string (file path) | required | matches ^\S+\.(bam|cram)$ |
pbi | string (file path) | optional | matches ^\S+\.(bai|crai|pbi)$ |
fail | string (file path) | optional | matches ^\S+\.(bam|cram)$ |
repeat_id | string | optional | — |
karyotype | string | optional | XXXY |
Required parameters
--inputstring (file path)Path to comma-separated file containing information about the samples in the experiment.
Constraint · matches ^\S+\.(csv|tsv|json|yaml|yml)$
--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
60 parameters · 10 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.
41 parameters · 19 hidden
Annotation6
Output directory where the downloaded VEP cache will be saved. Only used when --download_vep_cache true. Use absolute paths on cloud infrastructure. Note: when set, the cache is published outside --outdir.
Option to skip SNVs annotation with Ensembl VEP.
Add extra custom arguments to VEP for CNV annotation.
Add an extra custom argument to VEP.
Add extra custom arguments to VEP for SV annotation.
VEP output-file format.
General Workflow options1
Option to choose which workflow type to run
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.
Methylation Profiling3
Skip CpG site probability for 5mC methylation calling
Skip Fiber-seq nucleosome annotation with fibertools-rs
Skip fibertools-rs m6A prediction and use existing m6A calls for Fiber-seq nucleosome annotation
Pre Processing3
Fasta file of barcodes
Path to BED file containing intervals for either variant calling or for repeat expansion characterization
Option to skip demultiplexing
Reference Genome options11
Path to dbsnp VCF file
Path to index file of the dbsnp VCF file
Path to dict for variant calling
Download Ensembl VEP cache
Path to FASTA genome or MMI file.
Path to FASTA index
Name of iGenomes reference.
Path to VEP cache.
VEP cache version.
VEP genome.
VEP species.
Repeat1
If no sample-specific repeat ID to be plotted is provided in the samplesheet, this value will be used
Variant8
BED/BED.GZ file of regions to exclude from CNV calling.
BED/BED.GZ file specifying expected copy-number regions (for sawfish/hificnv).
Skip HiFiCNV copy number variant calling
Option to skip phasing
Option to skip SNP variant calling
Option to skip SV variant calling
The tool to use for calling SNP variants
The tool to use for calling structural variants
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/pacvar/blob/1.1.0/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.