pairgenomealign
nf-core/pairgenomealign
Pairwise alignment pipeline (genome to genome or reads to genome)
Key tools
Run it
nfclaw run pairgenomealign --input samplesheet.csv --outdir results --target <target> -profile dockernextflow run pipelines/pairgenomealign/upstream -profile docker --input samplesheet.csv --outdir results --target <target>nfclaw run pairgenomealign --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
sample | string | yes | matches ^\S+$ | |
fasta | string (file path) | yes | matches ^\S+\.f(ast|n)?(a|q)(\.gz)?$ |
--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):
sample,fastaFrom 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; fasta 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 pairgenomealign --input samplesheet.csv --outdir results --target <target> -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 pairgenomealign ... --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 pairgenomealign --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.
sample,fasta| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
sample | string | required | matches ^\S+$ |
fasta | string (file path) | required | matches ^\S+\.f(ast|n)?(a|q)(\.gz)?$ |
Required parameters
--targetstring (file path)Path or URL to a FASTA genome file for the _target_ genome.
Constraint · matches ^\S+\.fn?a(sta)?(\.gz)?$
--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
54 parameters · 8 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 · 19 hidden
Alignment options5
Mismap probability cutoff for last-split.
Arguments passed to both last-train and lastal.
Arguments passed only to lastal (useful when they are not recognised by last-train).
Path to a file containing alignment parameters or a scoring matrix. If this option is used, last-train will be skipped and alignment parameters will be the same for each query.
Make a many to many alignment
Dotplot Parameters10
Remove isolated alignments with the maf-filter tool.
Font size of the sequence names on the dot plots.
Maximum height of the dot plots, in pixels.
Extra arguments passed to last-dotplot to customise the output. See <gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst>.
Maximum width of the dot plots, in pixels.
Size of the alignments thumbnails in MultiQC (default 0 turns it off; 100 is a good value to start with).
Do not generate the many-to-many alignment dot-plot.
Do not generate the many-to-one alignment dot-plot.
Do not generate the one-to-many alignment dot-plot.
Do not generate the one-to-one alignment dot-plot.
Export options2
Convert the final _one-to-one_ alignment to a different format than MAF.
Produce a multi-query CRAM file combining all the alignments.
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).
Indexing options3
Select the LAST seed to index the _target_ genome.
Customise the way to mask the _target_ genome.
Index both strand, or just one.
Input Output options9
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.
Path or URL to a FASTA genome file for the _query_ genome.
Query genome name.
Skip assembly QC.
Path or URL to a FASTA genome file for the _target_ genome.
Target genome name.
Reference Genome options2
Path to FASTA genome file.
Name of iGenomes reference.
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/pairgenomealign/blob/3.0.4/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.