rnavar
nf-core/rnavar
GATK4 RNA variant calling pipeline
Key tools
Run it
nfclaw run rnavar --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/rnavar/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run rnavar --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
sample | string | no | 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+\.bai$ | |
cram | string (file path) | no | matches ^\S+\.cram$ | |
crai | string (file path) | no | matches ^\S+\.crai$ | |
vcf | string (file path) | no | matches ^\S+\.vcf\.gz$ | |
tbi | string (file path) | no | matches ^\S+\.vcf\.gz\.tbi$ | |
seq_platform | string | no | matches ^\S+$ | |
seq_center | string | no | matches ^\S+$ |
--input must match ^\S+\.(csv|tsv|yaml|yml|json)$.
The samplesheet is a CSV. Each row must include exactly one of these mutually-exclusive column groups (providing columns from more than one group fails validation):
sample,fastq_1sample,bamsample,cramsample,vcf
Fill each value per the table above and reference.md. Valid headers — pick the group that matches your data (optional columns from the table may be added):
sample,fastq_1sample,bamsample,cramsample,vcfFrom 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, vcf, tbi from files matching their patterns, by sample name. Set other columns with --sheet-set COLUMN=VALUE. Preview it with --check; a run records it in <outdir>/provenance/ for replay.
Reference genome
This release resolves a reference genome remotely by default. --genome defaults to GRCh38; the schema declares AWS iGenomes at s3://ngi-igenomes/igenomes/. The pinned configuration gives that key the FASTA ${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa. Resolving references through that default needs access to this source. For a self-contained run, pass your own reference instead (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 rnavar --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 = '!>=25.10.4'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run rnavar ... --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 rnavar --demo --outdir results # adds the upstream test profile (-profile test,docker)Samplesheet
A CSV. Each row uses exactly one of these column groups (columns from more than one fail validation) — pick the header that matches your data. Fill each value per the constraints below; optional columns from the table may be appended.
sample,fastq_1sample,bamsample,cramsample,vcf| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
sample | string | optional | 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+\.bai$ |
cram | string (file path) | optional | matches ^\S+\.cram$ |
crai | string (file path) | optional | matches ^\S+\.crai$ |
vcf | string (file path) | optional | matches ^\S+\.vcf\.gz$ |
tbi | string (file path) | optional | matches ^\S+\.vcf\.gz\.tbi$ |
seq_platform | string | optional | matches ^\S+$ |
seq_center | string | optional | matches ^\S+$ |
Required parameters
--inputstring (file path)Path to comma-separated file containing information about the samples in the experiment.
Constraint · matches ^\S+\.(csv|tsv|yaml|yml|json)$
--outdirstring (directory path)The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
--alignerstringSpecifies the alignment algorithm to use.
star--seq-platformstringSpecify the sequencing platform used
Parameter explorer
106 parameters · 11 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.
82 parameters · 24 hidden
Alignment options12
Specifies the alignment algorithm to use.
Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
Save the intermediate BAM files from the alignment step.
Where possible, save unaligned reads from aligner to the results directory.
Sequencing center information to be added to read group of BAM files.
Specify the sequencing platform used
Specifies the number of genome bins for coordinate-sorting
Do not use GTF file during STAR index building step
Specifies the maximum number of collapsed junctions
Specifies the maximum intron size
Option to limit RAM when sorting BAM file. Value to be specified in bytes. If 0, will be set to the genome index size.
Enable STAR 2-pass mapping mode.
General Reference Genome options3
Download annotation cache.
Do not load the iGenomes reference config.
Save built references.
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 options9
Specify whether to remove UMIs from the reads with UMI-tools extract. This parameter will be replaced with --tools umitools in future release.
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.
Save FastQ files after merging re-sequenced libraries in the results directory.
Skip the process of base recalibration steps i.e., GATK BaseRecalibrator and GATK ApplyBQSR.
Skip the check of the exon bed
Skip the process of preparing interval lists for the GATK variant calling step
Skip MultiQC reports
Skip variant filtering of GATK
Postprocessing1
Specify whether to remove duplicates from the BAM during Picard MarkDuplicates step.
Reference Genome options18
Path to dbsnp file.
Path to dbsnp index.
Path to FASTA dictionary file.
Path to BED file containing exon intervals. This will be created from the GTF file if not specified.
Path to FASTA genome file.
Path to FASTA reference index.
Type of feature to parse from annotation file
Name of iGenomes reference.
Path to GFF3 annotation file.
Path to GTF annotation file.
Path to known indels file.
Path to known indels file index.
Read length
snpEff DB version.
Path to STAR index folder or compressed file (tar.gz)
VEP cache version.
VEP genome.
VEP species.
Umitools options4
The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides of the read are from the UMI.
The UMI barcode pattern to use if the UMI is located in read 2.
UMI pattern to use. Can be either 'string' (default) or 'regex'.
The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software.
Variant Annotation21
A vcf file containing custom annotations to be used with bcftools annotate. Needs to be bgzipped.
Index file for bcftools_annotations
Optional text file with list of columns to use from bcftools_annotations, one name per row
Text file with the header lines of bcftools_annotations
Path to dbNSFP processed file.
Consequence to annotate with
Fields to annotate with
Path to dbNSFP tabix indexed file.
Path to snpEff cache.
Path to spliceai raw scores indel file.
Path to spliceai raw scores indel tabix indexed file.
Path to spliceai raw scores snv file.
Path to spliceai raw scores snv tabix indexed file.
Path to VEP cache.
Force preflight check for local VEP cache download
Add an extra custom argument to VEP.
Enable the use of the VEP dbNSFP plugin.
Enable the use of the VEP LOFTEE plugin.
Enable the use of the VEP SpliceAI plugin.
Enable the use of the VEP SpliceRegion plugin.
Should reflect the VEP version used in the container.
Variant Calling4
The minimum phred-scaled confidence threshold at which variants should be called.
Number of times the gene interval list to be split in order to run GATK haplotype caller in parallel
Enable generation of GVCFs by sample additionnaly to the VCFs.
Do not use gene interval file during variant calling
Variant Filtering4
The number of SNPs which make up a cluster. Must be at least 2.
Value to be used for the FisherStrand (FS) filter
Value to be used for the QualByDepth (QD) filter
The window size (in bases) in which to evaluate clustered SNPs.
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/rnavar/blob/1.3.0/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.