seqinspector
nf-core/seqinspector
Pipeline to QC your sequences
Key tools
Run it
nfclaw run seqinspector --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/seqinspector/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run seqinspector --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
sample | string | yes | matches ^\S+$ | |
fastq_1 | string (file path) | yes | matches ^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$ | |
fastq_2 | string (file path) | no | matches ^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$ | |
rundir | string | no | ||
tags | string | no | matches ^([A-Za-z0-9_-]+:)*([A-Za-z0-9_-]+)$ |
--input must match ^\S+\.csv$.
Additional row validation rules from the schema:
- When
fastq_2is set, also providefastq_1.
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,fastq_1Any of the optional columns above may be appended to the header when your data needs them: fastq_2, rundir, tags.
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; fastq_1/fastq_2 from FastQ files (mates paired by _R1/_R2, or by _1/_2 when their read names show they are mates); rundir 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 seqinspector --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 seqinspector ... --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 seqinspector --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,fastq_1| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
sample | string | required | matches ^\S+$ |
fastq_1 | string (file path) | required | matches ^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$ |
fastq_2 | string (file path) | optional | matches ^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$ |
rundir | string | optional | — |
tags | string | optional | matches ^([A-Za-z0-9_-]+:)*([A-Za-z0-9_-]+)$ |
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
51 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.
31 parameters · 20 hidden
Bbmap options2
Arguments to pass to BBMap Clumpify
Turn on saving of BBMap Clumpify deduplicated reads
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 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.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Take a subset of reads for analysis.
Comma-separated string of tools to skip - overrides any other means of tools selection
Comma-separated string of tools to run on subsampled data. Tools not in this list run on original data.
Comma-separated string of tools to run
Select some default setup for the tools to be run, tools can still be used to add tools
Kraken2 options4
Path to Kraken2 database file, either a gzipped file or the path to the uncompressed database.
Turn on saving of Kraken2 per-read taxonomic assignment file
Turn on saving of Kraken2-aligned reads
Turn on saving of uncompressed Kraken2 DB
Reference Genome options8
Path to bait intervals file.
Path to bwamem2 indices.
Sequence dictionary for the reference fasta file provided.
Fasta index for the reference fasta file provided.
Path to FASTA genome file.
A .csv of reference genomes to be mapped against by FastQ Screen
Name of iGenomes reference.
Path to target intervals file.
Riker options1
Arguments to pass to riker multi
Validation options3
Path to custom CheckQC config
Whether to continue with the pipeline if linting fails for a single sample.
Arguments to pass to FQ lint
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/seqinspector/blob/1.1.2/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.
Chaining
Run seqinspector as one stage of a chain: nfclaw chain run starts each stage only after the one before it succeeded, and prepares its inputs from that stage's outputs. Every rule is checked against both pinned schemas.
Fed by
- demultiplex — demultiplex writes samplesheet/seqinspector_samplesheet.csv for its demultiplexed FastQ files.
nfclaw chain edges seqinspector