createpanelrefs
nf-core/createpanelrefs
Generate Panel of Normals, models or other similar references from lots of samples
Key tools
Run it
nfclaw run createpanelrefs --input samplesheet.csv --outdir results --tools <tools> -profile dockernextflow run pipelines/createpanelrefs/upstream -profile docker --input samplesheet.csv --outdir results --tools <tools>nfclaw run createpanelrefs --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
sample | string | yes | matches ^\S+$ | |
bam | string (file path) | no | matches ^\S+\.bam$ | |
bai | string (file path) | no | matches ^\S+\.bai$ | |
cram | string (file path) | no | matches ^\S+\.cram$ | |
crai | string (file path) | no | matches ^\S+\.crai$ |
--input must match ^\S+\.csv$.
The samplesheet is a CSV. Each row must include exactly one of these mutually-exclusive column groups (providing columns from more than one group fails validation):
bamcram
Fill each value per the table above and reference.md. Valid headers — pick the group that matches your data (optional columns from the table may be added):
sample,bamsample,cramFrom 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; bam, bai, cram, crai from files matching their patterns, by sample name. 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 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 createpanelrefs --input samplesheet.csv --outdir results --tools <tools> -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 = '!>=26.04.0'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run createpanelrefs ... --nxf-ver 26.04.0--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run createpanelrefs --demo --outdir results # adds the upstream test profile (-profile test,docker)Samplesheet
A CSV. Each row uses exactly one of these column groups (columns from more than one fail validation) — pick the header that matches your data. Fill each value per the constraints below; optional columns from the table may be appended.
sample,bamsample,cram| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
sample | string | required | matches ^\S+$ |
bam | string (file path) | optional | matches ^\S+\.bam$ |
bai | string (file path) | optional | matches ^\S+\.bai$ |
cram | string (file path) | optional | matches ^\S+\.cram$ |
crai | string (file path) | optional | matches ^\S+\.crai$ |
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.
--toolsstringTools to use for building Panel of Normals or models.
Constraint · matches ^((cnvkit|germlinecnvcaller|gens|mutect2)?,?)*(?<!,)$
Parameter explorer
61 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.
41 parameters · 20 hidden
Cnvkit options4
Path to a gene annotation file used to label the CNVkit target regions.
Sequencing method used by CNVkit batch.
Name for panel of normals.
Path to directory for target file.
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).
Gens options7
GENS panel of normals analysis type ('srs' or 'lrs').
Length (in bp) of the bins. If zero, no binning will be performed.
Maximum chunk size when writing the HDF5 file
Minimum interval median percentile for gatk CreateReadCountPanelOfNormals
Run mosdepth with --fast-mode when computing long-read coverage ('lrs').
Name for panel of normals.
Output file format for count data
Germlinecnvcaller options6
Specifies which analysis type for the pipeline- either 'wgs' or 'wes'.
Length (in bp) of the bins. If zero, no binning will be performed.
Name for panel of normals.
Length (in bp) of the padding regions on each side of the intervals.
Output file format for count data
When scattering with this argument, each of the resultant files will (ideally) have this amount of interval-counts.
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.
Main options1
Tools to use for building Panel of Normals or models.
Mutect2 options2
Number of intervals.
Name for panel of normals.
Reference Genome options13
Path to sequence dictionary file
Path to fasta index file
Path to FASTA genome file.
Path to directory for a bed file containing regions to be exluded from the analysis.
Path to directory for exclude_interval_list file.
Path to Umap single-read mappability track in .bed or .bed.gz format. Overlapping intervals must be merged.
Path to a file containing ploidy priors table.
Path to segmental-duplication track in .bed or .bed.gz format. Overlapping intervals must be merged.
Path to directory for target bed file.
Path to directory for target interval_list file.
Name of iGenomes reference.
Path to GENS interval list file
Path to target bed file
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/createpanelrefs/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.