genomeqc
nf-core/genomeqc
A pipeline to compare multiple genomes and annotations
Key tools
Run it
nfclaw run genomeqc --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/genomeqc/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run genomeqc --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
assembly | string | yes | matches ^\S+$ | |
ncbi | string | no | matches ^GC[AF]_[0-9]{9}\.[0-9]+$ | |
fasta | string (file path) | no | matches ^\S+\.(fa|fasta|fna)(\.gz)?$ | |
gff | string (file path) | no | matches ^\S+\.(gff3?|gtf)(\.gz)?$ | |
fastq | string (file path) | no | matches ^\S+\.f(ast)?q(\.gz)?$ | |
taxid | integer | no |
--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):
assemblyAny of the optional columns above may be appended to the header when your data needs them: ncbi, fasta, gff, fastq, taxid.
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: assembly from file names; fastq from FastQ files (single-end); fasta, gff 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.
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 genomeqc --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 genomeqc ... --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 genomeqc --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.
assembly| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
assembly | string | required | matches ^\S+$ |
ncbi | string | optional | matches ^GC[AF]_[0-9]{9}\.[0-9]+$ |
fasta | string (file path) | optional | matches ^\S+\.(fa|fasta|fna)(\.gz)?$ |
gff | string (file path) | optional | matches ^\S+\.(gff3?|gtf)(\.gz)?$ |
fastq | string (file path) | optional | matches ^\S+\.f(ast)?q(\.gz)?$ |
taxid | integer | optional | — |
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
72 parameters · 12 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.
53 parameters · 19 hidden
Annotation options1
Tool for gxf validation.
Busco options7
Remove intermediate files
A path to a BUSCO config file (optional)
A flag to set the busco lineage.
A flag to set the BUSCO lineages directory (optional)
A string with NCBI taxonomic groups of the assemblies. Can be a comma-separated list.
Minimum number of Complete BUSCOs a sequence must have to be counted as significant ortholog-containing sequences.
Skip BUSCO. If run on genome only, it will also skip orthofinder.
Decontamination options5
Path to FCS-GX contamination screening database.
Path to FCS GX contamination screening database
Path to RAM-backed tmpfs or ramfs location to store FCS-GX database
Save cleaned genome after adaptor removal with FCS-GX
Save cleaned genome after decontamination with FCS-GX
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.
Orthology options3
OrthoFinder major version to run.
Publish longest protein isoform fasta files.
Publish orthofinder results.
Pipeline Mode options2
Container engine used to launch the interactive Shiny app. Only 'docker' and 'podman' are supported - Singularity/Apptainer does not work.
k-mer size for meryl (merqury).
Save Intermediate Files options5
Publish genomes and/or annotations of user-supplied RefSeq IDs.
Publish extracted protein fasta files by GFFREAD.
Publish filtered fasta genome files from seqkit.
Publish sorted fasta genome files from seqkit.
Publish gff files validated by AGAT.
Te Annotation options12
List of URLs to DFAM h5 partition files to download.
Download h5 partition files from the URLs specified in RM_db.
Path to a curated repeat library for HiTE.
Path to pre-staged famdb h5 partition file(s). Accepts a single file path or a glob pattern (e.g. '/path/FamDB*'). Alternative to downloading via RM_db.
Taxonomic lineage to filter repeat families from famdb (e.g. 'hymenoptera'). Omit to export all families.
Set to true for plant genomes (passed to HiTE).
RepeatMasker sensitivity/speed mode. 'default' is most sensitive; 'q' (quick) is ~5x faster; 'qq' (rush) is fastest with lowest sensitivity.
Run de novo repeat discovery with RepeatModeler before masking. Disabled by default — RepeatModeler typically requires 24 CPUs and 24–48 h per genome. When false, only the curated famdb library is used.
TE annotation method to run. Use 'hite' for HiTE or 'repeatmasker' for the full RepeatMasker pipeline. Omit to skip TE annotation. 'hite' does not support -profile conda/mamba - use -profile docker, -profile singularity, or -profile podman instead.
Minimum alignment coverage threshold (0.0–1.0) for repeat library clustering. Passed as -aS to CD-HIT-EST and -c (with --cov-mode 1) to MMseqs2.
Minimum sequence identity threshold (0.0–1.0) for repeat library clustering. Passed as -c to CD-HIT-EST and --min-seq-id to MMseqs2.
Clustering tool used to dereplicate the repeat library before RepeatMasker. 'mmseqs' uses MMseqs2 easy-cluster; 'linclust' (default) uses MMseqs2 easy-linclust (linear time, less sensitive); 'cdhit' uses CD-HIT-EST.
Tidk options2
DNA string for tidk motif search
Do not run TIDK.
Tree Summary options8
Circular layout only: which summary stats to draw as rings.
Circular layout only: phylogenetic-group thresholds used to score the quality (traffic-light) rings.
Circular layout only: override individual --quality_preset cut-offs.
Circular layout only: print each value on its ring.
Skip these stat plots in the genome and annotation tree plot.
Skip these stat plots in the genome only tree plot.
Modifies scale of the tree plot in the tree summary, default value is '0.0005'. Useful if tree tips overlap with the concatenated plots. Very sensitive, increase/decrease by two-fold.
Tree layout style for the tree summary plot.
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/genomeqc/blob/1.0.1/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.