Transcriptomicslatest-release

nanostring

nf-core/nanostring

Nanostring nCounter analysis pipeline

version1.3.36f0b2d537aJan 30, 2026 Upstream Usage docs

Key tools

MultiQCNACHOGSVASINGSCOREPLAGESSGSEASAMS

Run it

nfclaw

nfclaw run nanostring --input samplesheet.csv --outdir results -profile docker

raw nextflow

nextflow run pipelines/nanostring/upstream -profile docker --input samplesheet.csv --outdir results

demo · bundled test profile

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

Inputs

column	type	required	allowed values	constraints
`SAMPLE_ID`	string	yes		matches `^\S+$`
`RCC_FILE`	string (file path)	yes		matches `^\S+\.RCC$`
`RCC_FILE_NAME`	string	yes		matches `^\S+\.RCC$`
`TIME`	string or integer	no
`TREATMENT`	string or integer	no
`INCLUDE`	integer	no	`0`, `1`
`OTHER_METADATA`	string	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):

csv

SAMPLE_ID,RCC_FILE,RCC_FILE_NAME

Any of the optional columns above may be appended to the header when your data needs them: TIME, TREATMENT, INCLUDE, OTHER_METADATA.

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_ID from file names; RCC_FILE from files matching their patterns, by sample name. Set the required columns no file determines with --sheet-set COLUMN=VALUE (a constant or a {sample}/{lane} template): RCC_FILE_NAME (matching ^\S+.RCC$). 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 the reference_genome_options group in reference.md lists the reference options. 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:

bash

nfclaw run nanostring --input samplesheet.csv --outdir results -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 = '!>=25.10.2'.

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

bash

nfclaw run nanostring ... --nxf-ver 25.10.2

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

Demo

bash

nfclaw run nanostring --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.

samplesheet.csv header

SAMPLE_ID,RCC_FILE,RCC_FILE_NAME

Column	Type	Required	Allowed / constraints
`SAMPLE_ID`	string	required	matches ^\S+$
`RCC_FILE`	string (file path)	required	matches ^\S+\.RCC$
`RCC_FILE_NAME`	string	required	matches ^\S+\.RCC$
`TIME`	string or integer	optional	—
`TREATMENT`	string or integer	optional	—
`INCLUDE`	integer	optional	`01`
`OTHER_METADATA`	string	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

35 parameters · 8 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

15 parameters · 20 hidden

Gene Score Computation2

This selects the algorithm for computing the respective gene score. Default is 'plage.dir'.

This sets the YAML to be used for computing the gene scores. Needs both a name for each set of genes and respective genes to be selected.

Generic options6

Email address for completion summary.

Display the help message.

Display the full detailed help message.

Custom MultiQC yaml file containing HTML including a methods description.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Display hidden parameters in the help message (only works when --help or --help_full are provided).

Input Output options2

Path to comma-separated file containing information about the samples in the experiment.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Normalization Parameters1

The method to use for normalization of nCounter data.

Processing options2

Path to YAML file (list, one item per line) to specify which genes should be used for the gene-count heatmap.

The column used for heatmap generation, specifying the rows. The values in this column have to be unique.

Reference Genome options1

Name of iGenomes reference.

Skipping options1

Skip creating the heatmap

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/nanostring/blob/1.3.3/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.