nanoseq
nf-core/nanoseq
A pipeline to demultiplex, QC and map Nanopore data
Key tools
Run it
nfclaw run nanoseq --input samplesheet.csv --outdir results --protocol <protocol> -profile dockernextflow run pipelines/nanoseq/upstream -profile docker --input samplesheet.csv --outdir results --protocol <protocol>nfclaw run nanoseq --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
Pinned input correction. The bundled FASTQ schema is a stale template. The pinned checker requires the six columns below in this exact order. Input data may be FASTQ, BAM or a FAST5 directory; fasta may be a local reference path or a configured genome key. Empty optional cells retain their place in the CSV header. Write the sheet explicitly and review barcode, replicate and reference assignments.
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
group | string | yes | matches ^\S+$ | |
replicate | integer | yes | matches ^\d+$; ≥ 1 | |
barcode | string | no | matches ^\d+$ | |
input_file | string (file or directory path) | no | ||
fasta | string | no | ||
gtf | string (file path) | no | matches ^\S+\.gtf(\.gz)?$ |
--input must match ^\S+\.csv$.
The samplesheet is a CSV with this header (the required header order; optional values may be empty); fill each value per the table above and reference.md (no example value is invented here):
group,replicate,barcode,input_file,fasta,gtfFrom data files. nfclaw cannot generate this samplesheet: group, replicate, barcode, data layout and reference assignments require an explicit samplesheet.
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 nanoseq --input samplesheet.csv --outdir results --protocol <protocol> -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 = '!>=22.10.1'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run nanoseq ... --nxf-ver 22.10.1--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Nextflow 22.10.1 predates process.resourceLimits (24.04.0), so --limit-* cannot be combined with this pin — nfclaw refuses it rather than run without the ceiling; cap resources with the release's own --max-cpus, --max-memory, --max-time instead.
Demo
nfclaw run nanoseq --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.
group,replicate,barcode,input_file,fasta,gtf| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
group | string | required | matches ^\S+$ |
replicate | integer | required | matches ^\d+$; ≥ 1 |
barcode | string | optional | matches ^\d+$ |
input_file | string (file or directory path) | optional | — |
fasta | string | optional | — |
gtf | string (file path) | optional | matches ^\S+\.gtf(\.gz)?$ |
Required parameters
--inputstring (file path)Path to comma-separated file containing information about the samples in the experiment.
Constraint · matches ^\S+\.csv$
--protocolstringInput sample type. Valid options: 'DNA', 'cDNA', and 'directRNA'.
Parameter explorer
64 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.
42 parameters · 22 hidden
Alignment options4
Specifies the aligner to use i.e. 'minimap2' or 'graphmap2'.
Save the '.sam' files from the alignment step - not done by default.
Skip alignment and downstream processes.
Specifies if the data is strand-specific. Automatically activated when using '--protocol directRNA'.
Demultiplexing options11
Require barcode on both ends for basecaller.
Barcode kit used to perform the sequencing e.g. 'SQK-PBK004'.
Cluster options required to use GPU resources (e.g. '--part=gpu --gres=gpu:1').
Device specified in GPU mode using '--device'.
Path to Nanopore run directory files (e.g. 'fastq_pass/*') or a basecalled fastq file that requires demultiplexing.
Fasta file to be filtered against using NanoLyse
Search for adapters in the whole read by applying the '--detect-middle' parameter in qcat.
Specify the minimum quality score for qcat in the range 0-100.
Filter reads from FastQ files using NanoLyse
Skip demultiplexing with qcat.
Trim barcodes from the output sequences in the FastQ files from basecaller.
Differential Analysis options3
Specifies the transcript quantification method to use (available are: bambu or stringtie2). Only available when protocol is cDNA or directRNA.
Skip differential analysis with DESeq2 and DEXSeq.
Skip transcript quantification and differential analysis.
Input Output options5
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.
Input sample type. Valid options: 'DNA', 'cDNA', and 'directRNA'.
Process Skipping options6
Skip BigBed file generation.
Skip BigWig file generation.
Skip FastQC.
Skip MultiQC.
Skip NanoPlot.
Skip all QC steps apart from MultiQC.
Rna Fusion Analysis options2
Specifies the reference directory for JAFFAL.
Skip differential analysis with DESeq2 and DEXSeq.
Rna Modification Analysis options3
Skip m6A detection with m6anet.
Skip RNA modification analysis.
Skip differential modification analysis with xpore.
Variant Calling options8
Specifies if variant calling will executed.
Specifies whether to call variants with pepper_margin_deepvariant in GPU mode.
Specifies if vcf will be phased when using medaka.
Skip structural variant calling.
Skip variant calling.
Specifies if MNPs will be split into SNPs when using medaka.
Specifies the variant caller that will be used to call structural variants (available are: sniffles and cutesv). Structural variant calling is only available if '--call_variants' is set and the protocol is set to DNA.
Specifies the variant caller that will used to call small variants (available are: medaka, deepvariant, and pepper_margin_deepvariant). Variant calling is only available if '--call_variants' is set and the protocol is set to DNA. Please note deepvariant and pepper_margin_deepvariant are only avaible if using singularity or docker.
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/nanoseq/blob/3.1.0/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.