rnadnavar
nf-core/rnadnavar
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
Key tools
Run it
nfclaw run rnadnavar --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/rnadnavar/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run rnadnavar --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
patient | string | yes | matches ^\S+$ | |
sample | string | yes | matches ^\S+$ | |
status | integer | no | ≥ 0; ≤ 2 | |
lane | string | no | matches ^\S+$ | |
fastq_1 | string (file path) | no | matches ^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$ | |
fastq_2 | string (file path) | no | ||
table | string (file path) | no | ||
cram | string (file path) | no | ||
crai | string (file path) | no | ||
bam | string (file path) | no | ||
bai | string (file path) | no | ||
vcf | string (file path) | no | ||
variantcaller | string | no | ||
maf | string (file path) | no | ||
normal_id | string | no | matches ^\S+$ |
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):
patient,sampleAny of the optional columns above may be appended to the header when your data needs them: status, lane, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf, normal_id.
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); lane from Illumina lane numbers (_L002 → 2, else 1); table, cram, crai, bam, bai, vcf, maf from files matching their patterns, by sample name. Optional columns left out take their schema defaults in the pipeline: status = 1 — set them with --sheet-set where your design differs. Set the required columns no file determines with --sheet-set COLUMN=VALUE (a constant or a {sample}/{lane} template): patient (matching ^\S+$). 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 rnadnavar --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 rnadnavar ... --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 rnadnavar --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.
patient,sample| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
patient | string | required | matches ^\S+$ |
sample | string | required | matches ^\S+$ |
status | integer | optional | ≥ 0; ≤ 2 |
lane | string | optional | matches ^\S+$ |
fastq_1 | string (file path) | optional | matches ^([\S\s]*\/)?[^\s\/]+\.f(ast)?q\.gz$ |
fastq_2 | string (file path) | optional | — |
table | string (file path) | optional | — |
cram | string (file path) | optional | — |
crai | string (file path) | optional | — |
bam | string (file path) | optional | — |
bai | string (file path) | optional | — |
vcf | string (file path) | optional | — |
variantcaller | string | optional | — |
maf | string (file path) | optional | — |
normal_id | string | optional | matches ^\S+$ |
Required parameters
--inputstringPath to comma-separated file containing information about the samples in the experiment.
--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
126 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.
56 parameters · 70 hidden
Alignment options4
Specify aligner to be used to map reads to reference genome.
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.
Fastq Preprocessing1
Run FastP for read trimming
Filtering9
Path to BED file with positions to blacklist during filtering (e.g. regions difficult to map)
Chain file to do liftover - only if secondary_pon is provided
RNA filtering - name of the primary reference being used (e.g. hg38)
Path to the primary RNA PoN used for RNA-specific filtering (see DOI: 10.1016/j.cels.2018.03.002)
Path to BED files with RNA editing sites, comma separated if more than one
Path to the optional secondary RNA PoN used for RNA-specific filtering (see DOI: 10.1016/j.cels.2018.03.002)
Path to the optional secondary reference FASTA - only if secondary_pon is provided
RNA filtering - name of the secondary reference being used (e.g. hg19) - only if secondary_pon is provided
Path to BED file with variants to whitelist during filtering
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
True if there are DNA samples to be analysed
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.
True if there are RNA samples to be analysed
Save mapped BAMs.
Save mapped files.
Saves output from Markduplicates & Baserecalibration as BAM file instead of CRAM
Specify how many reads each split of a FastQ file contains. Set 0 to turn off splitting at all.
Starting step
Pipeline Stage options3
Disable specified tools.
Tools to use for variant calling and/or for annotation.
Enable when exome or panel data is provided.
Reference Genome options20
Only built references.
Download annotation cache.
Path to FASTA genome file.
Path to FASTA reference index.
Name of iGenomes reference.
Path to GFF3 annotation file.
Path to GTF annotation file.
Minimum memory required to use splice sites and exons in the HiSAT2 index build process.
Path to STAR index folder or compressed file (tar.gz)
If you use AWS iGenomes, this has already been set for you appropriately. Path to known snps file.
Path to known snps file snps.
Estimate interval size.
Read length
Save built references.
Splice sites file required for HISAT2.
Do not use GTF file during STAR index buidling step
Path to STAR index folder or compressed file (tar.gz)
Specifies the maximum number of collapsed junctions
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.
Variant Calling4
Variant callers used to generate calls
Path to target bed file in case of whole exome or targeted sequencing or intervals file.
Runs Mutect2 in joint (multi-sample) mode for better concordance among variant calls of tumor samples from the same patient. Mutect2 outputs will be stored in a subfolder named with patient ID under variant_calling/mutect2/ folder. Only a single normal sample per patient is allowed. Tumor-only mode is also supported.
Disable usage of intervals.
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/rnadnavar/blob/1.0.0/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.