stableexpression
nf-core/stableexpression
This pipeline is dedicated to identifying the most stable genes within a single or multiple expression dataset(s). This is particularly useful for identifying the most suitable RT-qPCR reference genes for a specific species.
Key tools
Run it
nfclaw run stableexpression --outdir results -profile dockernextflow run pipelines/stableexpression/upstream -profile docker --outdir resultsnfclaw run stableexpression --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
This pipeline does not use a samplesheet; configure inputs via parameters.
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 stableexpression --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 = '!>=26.04.4'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run stableexpression ... --nxf-ver 26.04.4--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run stableexpression --demo --outdir results # adds the upstream test profile (-profile test,docker)Required parameters
--outdirstring (directory path)Output directory
Parameter explorer
60 parameters · 10 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.
43 parameters · 17 hidden
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).
Idmapping options7
Custom gene id mapping file
Custom gene metadata file
Experimental: target database for g:Profiler
Minimum frequency of occurrence among all datasets
Minimum quantile for the frequency of occurrence
Skip cleaning gene IDs step
Skip g:Profiler ID mapping step
Input Output options11
Only get accessions from Expression Atlas / GEO and exit.
Custom datasets (counts + designs)
Only get accessions from Expression Atlas / GEO and download the selected datasets.
Email address for completion summary.
Keywords used for selecting specific Expression Atlas / GEO accessions
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
Output directory
Only download from this platform
Scientifc species name (genus and species)
File containing target genes
Target genes
Missing Value Imputation options1
Type of imputation method to use for missing values
Normalisation options5
Gene length file
Genome annotation file (GFF format)
URL to genome annotation file (GFF format)
Count normalisation method
Target distribution for quantile normalisation
Public Data options6
Expression Atlas / GEO accession(s) to include
File containing Expression Atlas / GEO accession(s) to download
Expression Atlas accession(s) to exclude
File containing Expression Atlas accession(s) to exclude
Fetch GEO accessions from NCBI [Experimental]
Skip fetching Expression Atlas accessions
Sample Filtering options3
Maximum ratio of null values
Maximum ratio of null values in a sample for it to be considered in the computation of the null value malus
Maximum ratio of zero counts to total counts
Scalability options2
Seed for dataset random sampling.
Number of public dataset samples to choose randomly before downloading.
Stability Scoring options4
Number of candidate genes to keep for stability scoring in each section
Number of sections to divide genes into for stability scoring.
Run Genorm
Weights for stability score calculation
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/stableexpression/blob/1.1.0/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.