phaseimpute
nf-core/phaseimpute
Phasing and imputation pipeline
Key tools
Run it
nfclaw run phaseimpute --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/phaseimpute/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run phaseimpute --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
sample | string | yes | matches ^[a-zA-Z0-9_-]+$ | |
tools | string | no | matches ^[a-zA-Z0-9_]+$ | |
file | string | yes | matches ^\S+\.(bam|cram)|((vcf|bcf)(\.gz))?$ | |
index | string | yes | matches ^\S+\.(bai|crai|tbi|csi)$ |
--input must match ^\S+\.(csv|tsv|yaml|json)$.
For tabular CSV/TSV input, use this header (the columns the schema requires); fill each value per the table above and reference.md (no example value is invented here):
sample,file,indexAny of the optional columns above may be appended to the header when your data needs them: tools.
From data files. --input may also be the data files — a directory (searched recursively), a quoted glob, or files (--input once per file) — from which nfclaw writes this samplesheet: sample from file names; index from files matching their patterns, by sample name. Set the required columns no file determines with --sheet-set COLUMN=VALUE (a constant or a {sample}/{lane} template): file (matching ^\S+.(bam|cram)|((vcf|bcf)(.gz))?$). 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 phaseimpute --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 = '!>=25.04.0'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run phaseimpute ... --nxf-ver 25.04.0--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run phaseimpute --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,file,index| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
sample | string | required | matches ^[a-zA-Z0-9_-]+$ |
tools | string | optional | matches ^[a-zA-Z0-9_]+$ |
file | string | required | matches ^\S+\.(bam|cram)|((vcf|bcf)(\.gz))?$ |
index | string | required | matches ^\S+\.(bai|crai|tbi|csi)$ |
Required parameters
--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
58 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.
35 parameters · 23 hidden
Generic options6
Display the help message.
Display the full detailed help message.
Custom MultiQC yaml file containing HTML including a methods description.
Optional two-column sample renaming file. First column a set of patterns, second column a set of corresponding replacements. Passed via MultiQC's --replace-names option.
Optional TSV file with headers, passed to the MultiQC --sample_names argument.
Display hidden parameters in the help message (only works when --help or --help_full are provided).
Imputation options3
Maximal number of individuals per batch for imputation.
Path to comma or tab-separated file, yaml or json file containing genomic chunks to be used for imputation.
Path to comma or tab-separated file, yaml or json file containing reference panel information converted files for imputation.
Input Output options9
Email address for completion summary.
Path to comma or tab-separated file, yaml or json file containing information about the samples in the experiment.
Path to comma or tab-separated file, yaml or json file containing region of the genome to use (optional: if no file given, the whole genome will be used).
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.
Comma-separated list of samples to remove from the reference panel. Useful for benchmarking purposes.
Should the panel VCF files be renamed to match the reference genome (e.g. 'chr1' -> '1')
Step(s) to run.
Imputation tool to use.
Panelprep4
Should the allele frequency for each variant (AC/AN fields necessary for Glimpse1 and the validation step) be computed using VCFFIXUP tool. This can be necessary if the fields are absent from the panel or if samples have been removed.
Should the reference panel be normalized
Path to comma or tab-separated file, yaml or json file containing reference panel information.
Should the reference panel be phased
Quilt Parameters2
Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd.
Number of generations since founding of the population to use for imputation.
Reference Genome options4
Path to FASTA genome file.
Path to FASTA index genome file.
Name of iGenomes reference.
Path to gmap genome file.
Simulate2
Depth of coverage for the simulated data
Genotype position to use to simulate the data
Stitch Parameters1
Number of ancestral haplotypes to use for imputation. Refer to the documentation for the --K argument of STITCH for more information.
Validation4
User-defined allele count bins used for rsquared computations.
Path to comma or tab-separated file, yaml or json file containing samples truth files informations.
Minimum coverage in validation data. If FORMAT/DP is missing and -min_val_dp > 0, the program exits with an error. Set to zero to have no filter of if using –gt-validation
Minimum genotype likelihood probability P(G|R) in validation data. Set to zero to have no filter, if using gt-validation
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/phaseimpute/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.