Single-cell & spatiallatest-release

scnanoseq

nf-core/scnanoseq

Single-cell/nuclei pipeline for data derived from Oxford Nanopore

version1.3.083d55ea87eJun 26, 2026 Upstream Usage docs

Key tools

BLAZEFastQCIsoQuantMinimap2MultiQCNanoCompChopperNanoPlotoarfishpigzSAMtoolsToulligQCUMI-toolsPicardUCSC toolsRggplot2optparseSeuratBiopythonNumPyPandasPysam

Run it

nfclaw

nfclaw run scnanoseq --input samplesheet.csv --outdir results --gtf <gtf> --barcode-format <barcode_format> --quantifier <quantifier> -profile docker

raw nextflow

nextflow run pipelines/scnanoseq/upstream -profile docker --input samplesheet.csv --outdir results --gtf <gtf> --barcode_format <barcode_format> --quantifier <quantifier>

demo · bundled test profile

nfclaw run scnanoseq --demo --outdir results   # adds the upstream test profile (-profile test,docker)

Inputs

column	type	required	constraints
`sample`	string	yes	matches `^\S+$`
`fastq`	string (file path)	yes	matches `^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$`
`cell_count`	integer	yes

--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):

csv

sample,fastq,cell_count

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 from FastQ files (single-end). Set the required columns no file determines with --sheet-set COLUMN=VALUE (a constant or a {sample}/{lane} template): cell_count (integer). 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 iGenomes lookup is disabled by default (--igenomes-ignore true). Configure your reference explicitly (the reference_genome_options group in reference.md lists the reference options). 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:

bash

nfclaw run scnanoseq --input samplesheet.csv --outdir results --gtf <gtf> --barcode-format <barcode_format> --quantifier <quantifier> -profile docker \
  --limit-cpus 4 --limit-memory 15.GB

nfclaw 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 = '!>=25.04.2'.

To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:

bash

nfclaw run scnanoseq ... --nxf-ver 25.04.2

--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.

Demo

bash

nfclaw run scnanoseq --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.

samplesheet.csv header

sample,fastq,cell_count

Column	Type	Required	Allowed / constraints
`sample`	string	required	matches ^\S+$
`fastq`	string (file path)	required	matches ^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$
`cell_count`	integer	required	—

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.

--gtfstring (file path)

Path to GTF file.

Constraint · matches ^\S+\.gtf(\.gz|\.zip)?$

--barcode-formatstring

Specify the format for the barcode+umi. This parameter also defines a default barcode whitelist for the pipeline to use for barcode calling, this can be overridden with the 'whitelist' parameter.

10X_3v310X_3v410X_5v210X_5v3

--dedup-toolstring

Specify which tool to be used for deduplication (Options: picard, umitools)

umitoolspicard

--quantifierstring

Provide a comma-delimited options of quantifiers for the pipeline to use. Available tools: isoquant, oarfish

Constraint · matches ^(oarfish|isoquant)(,(oarfish|isoquant))*$

Parameter explorer

58 parameters · 10 groups

Every 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.

Groups

nextflow_schema.json

38 parameters · 20 hidden

Analysis options2

Provide a comma-delimited options of quantifiers for the pipeline to use. Available tools: isoquant, oarfish

Indicate whether to include introns in the count matrices

Cell Barcode options4

Specify the format for the barcode+umi. This parameter also defines a default barcode whitelist for the pipeline to use for barcode calling, this can be overridden with the 'whitelist' parameter.

Specify which tool to be used for deduplication (Options: picard, umitools)

Do not perform the demultiplexing step in BLAZE (conserves time and disk space).

User-provided file containing a list of cellular barcodes. Using this parameter will override the default whitelists provided by the pipeline and use the user-provided one instead.

Fastq options1

The number of lines to split the FASTQ into.

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.

Mapping4

Minimizer k-mer length.

Save the secondary alignments when aligning to the genome

Save the secondary alignments when aligning to the transcriptome

Library strandness option.

Process Skipping options11

Skip NanoComp from BAM file(s).

Skip umi dedup.

Skip NanoComp from FASTQ file(s).

Skip FastQC.

Skip MultiQC.

Skip Nanoplot.

Skip all QC.

Skip RSeQC.

Skip saving minimap2 index.

Skip Seurat QC.

Skip ToulligQC.

Read Trimming options3

Choose minimum read length.

Choose minimum average read quality score.

Skip quality trimming step.

Reference Genome options5

This is the delimiter the FASTA uses in the sequence identifier to separate the string.

Name of iGenomes reference.

Path to genome FASTA file.

Path to GTF file.

Path to transcriptome FASTA 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. --skip-multiqc true disables that report. 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/scnanoseq/blob/1.3.0/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.