smrnaseq
nf-core/smrnaseq
Small RNA-Seq Best Practice Analysis Pipeline.
Key tools
Run it
nfclaw run smrnaseq --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/smrnaseq/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run smrnaseq --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$ |
--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):
sample,fastq_1Any of the optional columns above may be appended to the header when your data needs them: fastq_2.
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). 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 smrnaseq --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 = '!>=25.04.2'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run smrnaseq ... --nxf-ver 25.04.2--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run smrnaseq --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$ |
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
71 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.
52 parameters · 19 hidden
Contamination Filtering7
Path to the cDNA fasta file to be used as contamination database.
Enables the contamination filtering.
Path to the ncRNA fasta file to be used as contamination database.
Path to an additional fasta file to be used as contamination database.
Path to the piRNA fasta file to be used as contamination database.
Path to the rRNA fasta file to be used as contamination database.
Path to the tRNA fasta file to be used as contamination database.
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 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.
Save all intermediate files (e.g. fastq, bams) of all steps of the pipeline to output directory
Reference Genome options14
Path to a Bowtie 1 index directory
Path to FASTA genome file.
Name of iGenomes reference.
Path to FASTA file with miRNAs precursors.
Directory / URL base for iGenomes references.
Path to FASTA file with mature miRNAs.
Boolean whether MirGeneDB should be used instead of miRBase
GFF/GTF file with coordinates positions of precursor and miRNAs.
Path to FASTA file with miRNAs precursors.
Path to FASTA file with MirGeneDB mature miRNAs.
Species of MirGeneDB.
GFF/GTF file with coordinates positions of precursor and miRNAs.
Species for miRTrace.
Save generated reference genome files to results.
Skipping Pipeline Steps4
Skip FastP
Skip FastQC
Skip miRDeep
Skip MultiQC
Trimming options11
The number of basepairs to remove from the 5' end of read 1.
Fasta with known miRNA adapter sequences for adapter trimming
Maximum filter length for raw reads.
Minimum filter length for raw reads.
Minimum number of reads required in input file to use it
The PHRED quality offset to be used for any input fastq files. Default is 33, standard Illumina 1.8+ format.
Save merged reads.
Save reads failing trimming
Sequencing adapter sequence to use for trimming.
The number of basepairs to remove from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
Trim FastQ files
Umi options7
If this option is specified, intermediate FastQ and BAM files produced by UMI-tools are also saved in the results directory.
Skip the UMI extraction from the reads before deduplication. Please note, if this parameter is set to false, the reads will be deduplicated solely on insert sequence. UMIs might be extracted after deduplication depending on the set umitools_bc_pattern nevertheless if with_umi is set to True.
After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively.
The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides of the read are from the UMI.
UMI pattern to use. Can be either 'string' (default) or 'regex'.
UMI grouping method
Enable UMI-based read deduplication.
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/smrnaseq/blob/2.4.1/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.