rnafusion
nf-core/rnafusion
Nextflow rnafusion analysis pipeline, part of the nf-core community.
Key tools
Run it
nfclaw run rnafusion --input samplesheet.csv --outdir results --genomes-base <genomes_base> --tools <tools> -profile dockernextflow run pipelines/rnafusion/upstream -profile docker --input samplesheet.csv --outdir results --genomes_base <genomes_base> --tools <tools>nfclaw run rnafusion --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) | no | matches ^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$ | |
fastq_2 | string (file path) | no | matches ^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$ | |
bam | string (file path) | no | matches ^\S+\.bam$ | |
bai | string (file path) | no | matches ^\S+\.bam\.bai$ | |
cram | string (file path) | no | matches ^\S+\.cram$ | |
crai | string (file path) | no | matches ^\S+\.cram\.crai$ | |
junctions | string (file path) | no | matches ^\S+\.junction$ | |
splice_junctions | string (file path) | no | matches ^\S+\.SJ.out.tab$ | |
strandedness | string | yes | forward, reverse, unstranded, unknown | |
seq_platform | string | no | matches ^\S+$ | |
seq_center | string | no | matches ^\S+$ |
--input must match ^\S+\.(csv|yaml|yml|json)$.
Additional row validation rules from the schema:
- When
baiis set, also providebam. - When
craiis set, also providecram.
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,strandednessAny of the optional columns above may be appended to the header when your data needs them: fastq_1, fastq_2, bam, bai, cram, crai, junctions, splice_junctions, seq_platform, seq_center.
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); bam, bai, cram, crai, junctions, splice_junctions 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): strandedness (one of forward, reverse, unstranded, unknown). 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. A genome name alone does not specify where reference files come from. Confirm the selected reference's paths and source in the pinned upstream/nextflow.config and upstream/conf/ before running. To supply your own reference, use e.g. --fasta; the reference_genome_options group in reference.md lists every reference option.
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 rnafusion --input samplesheet.csv --outdir results --genomes-base <genomes_base> --tools <tools> -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 = '!>=25.10.4'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run rnafusion ... --nxf-ver 25.10.4--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run rnafusion --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,strandedness| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
sample | string | required | matches ^\S+$ |
fastq_1 | string (file path) | optional | matches ^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$ |
fastq_2 | string (file path) | optional | matches ^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$ |
bam | string (file path) | optional | matches ^\S+\.bam$ |
bai | string (file path) | optional | matches ^\S+\.bam\.bai$ |
cram | string (file path) | optional | matches ^\S+\.cram$ |
crai | string (file path) | optional | matches ^\S+\.cram\.crai$ |
junctions | string (file path) | optional | matches ^\S+\.junction$ |
splice_junctions | string (file path) | optional | matches ^\S+\.SJ.out.tab$ |
strandedness | string | required | forwardreverseunstrandedunknown |
seq_platform | string | optional | matches ^\S+$ |
seq_center | string | optional | matches ^\S+$ |
Required parameters
--outdirstring (directory path)The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
--genomes-basestringPath to reference folder
--toolsstringComma-delimited list of tools to run
Constraint · matches ^((arriba|ctatsplicing|fusioncatcher|starfusion|stringtie|fusionreport|fastp|salmon|fusioninspector|all)?,?)*(?<!,)$
Parameter explorer
85 parameters · 7 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.
67 parameters · 18 hidden
Compression options1
Output CRAM files instead of BAM files.
Generic options6
Display the full detailed help message.
Custom MultiQC yaml file containing HTML including a methods description.
Sequencing center, used to fill in read group CN tag in the BAM header
Sequencing platform, used to fill in read group PL tag in the BAM header
Display hidden parameters in the help message (only works when --help or --help_full are provided).
The maximum amount of RAM to use for sorting the BAM file in STAR. Should by in bits. Setting this value to 0 will use the default amount of STAR.
Input Output options39
URL to annotation filter rule file
Path to arriba output
Path to arriba reference blacklist
Path to arriba reference cytobands
Path to arriba reference known fusions
Path to arriba reference protein domain
COSMIC password
COSMIC username
Path to the cancer introns CSV file to create the CTAT-SPLICING reference with
Path to Dfam H3F database file
Path to Dfam H3I database file
Path to Dfam H3M database file
Path to Dfam H3P database file
Path to Dfam HMM database file
Email address for completion summary.
Path to fusioncatcher output
Use limitSjdbInsertNsj with int for fusioncatcher
Path to fusioncatcher references
Path to a fusion list file built with format GENE1--GENE2
Use limitSjdbInsertNsj with int for fusioninspector STAR process
Path to fusionreport references
gencode version
Path to reference folder
Don't automatically assign reference parameters to the correct references in --genomes_base
Path to HGNC timestamp file for database retrieval
Path to HGNC database file
Path to samplesheet 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.
Path to Pfam database file
Use QIAGEN instead of SANGER to download COSMIC database
The length of the reads provided to the pipeline. This is used for the '--sjdbOverhang' option of STAR as read_length - 1. Providing 1 to this option will disable overhang handling.
Path to salmon index
Path to starfusion output
Path to starfusion references
Path to starindex references
Comma-delimited list of tools to run
Discard fusions identified by less than INT tools
Path to fusions to add to the input of fusioninspector
Read Trimming options6
Path to adapter fasta file: default: []
FASTP: Inputs with fewer than this reads will be filtered out of the "reads" output channel
FASTP: Specify true to save merged reads
FASTP: Specify true to save files that failed to pass trimming thresholds
The amount of bases to trim at the tail of each read, none will be trimmed by default
The amount of bases to trim at the tail of each read for fusioncatcher, none will be trimmed by default
Reference Genome options12
Version of dfam to use
Path to FASTA genome index file.
Path to FASTA genome file.
Path to Fusion Annotation Library to be used in STARFUSION_BUILD.
Name of iGenomes reference.
Path to GTF genome file.
Avoid using Cosmic DB (for example in clinical case applications where a paid license applies.
Version of pfam to use
Skip running the analysis, only builds the references
Path to GTF genome file.
Path to ribosomal interval list.
Which species dfam should automatically download, default: homo_sapiens.
Skip Steps3
Skip QC steps
Skip vcf creation step
Skip visualisation steps
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/rnafusion/blob/4.1.3/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.