oncoanalyser
nf-core/oncoanalyser
A comprehensive cancer DNA/RNA analysis and reporting pipeline
Key tools
Run it
nfclaw run oncoanalyser --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/oncoanalyser/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run oncoanalyser --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
Pinned input contract. For FASTQ rows, filepath is forward_path;reverse_path and both members must be absolute local paths or explicit remote URLs. File-type selection is case-insensitive. Other file types use one file or directory location. FASTQ info must provide library_id and lane; review their assignments against the study design. The group_id, subject_id and filename-forming info values (library_id, lane, flowcell) receive the same literal alias checks as sample identifiers. Info keys follow the consumer's uppercase normalization. An apostrophe in read_group_overrides is refused because the pinned BWA command passes its read-group line in single quotes. The exact compound interpretation is guarded by the pinned revision and consumer source hashes.
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
group_id | string | yes | matches ^\S+$ | |
subject_id | string | yes | matches ^\S+$ | |
sample_id | string | yes | matches ^\S+$ | |
sample_type | string | yes | normal, tumor, donor, tumor_normal | matches ^\S+$ |
sequence_type | string | yes | dna, rna, dna_rna | matches ^\S+$ |
info | string | no | matches ^\S+$ | |
filetype | string | yes | matches ^\S+$ | |
filepath | string | yes | matches ^\S+$ |
--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):
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepathAny of the optional columns above may be appended to the header when your data needs them: info.
From data files. nfclaw cannot generate this samplesheet: the samplesheet declares no file type nfclaw could match files against (no column's pattern names a file extension).
Reference genome
No reference genome is set by default: supply your own reference. The iGenomes lookup is disabled by default (--igenomes-ignore true). Configure your reference explicitly (the reference_data_options group in reference.md lists the reference options). 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 oncoanalyser --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 oncoanalyser ... --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 oncoanalyser --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.
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
group_id | string | required | matches ^\S+$ |
subject_id | string | required | matches ^\S+$ |
sample_id | string | required | matches ^\S+$ |
sample_type | string | required | normaltumordonortumor_normalmatches ^\S+$ |
sequence_type | string | required | dnarnadna_rnamatches ^\S+$ |
info | string | optional | matches ^\S+$ |
filetype | string | required | matches ^\S+$ |
filepath | string | required | 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.
Parameter explorer
75 parameters · 5 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.
51 parameters · 24 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).
Input Output options2
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.
Other options34
Create placeholders for reference data during stub run.
User defined driver gene panel used in panel resource creation, or for overriding the default file located in ref_data_hmf_data_path
Email address for completion summary.
During panel resource creation, calculate copy number normalisation factors based on per-region copy number percentiles derived from the Hartwig WGS solid tumor cohort.
Enable fastp UMI processing.
fastp UMI length parameter (--umi_len)
fastp UMI location parameter (--umi_loc).
fastp UMI skip parameter (--umi_skip)
UMI delimiter fastq-tools.
Enable fastq-tools UMI processing.
Skip check for restricted genome.
Skip check for known panels.
Path to GRIDSS configuration file.
Log level filter for WiGiTS modules
User defined Isofox expected counts files (read length dependent).
Semicolon-separated list of Isofox functions to run
User defined Isofox expected GC ratios file.
User defined Isofox gene list file for panel data.
User defined RNA read length used for Isofox.
User defined Isofox TPM normalisation file for panel data.
When positive, parallelise read alignment across multiple jobs by splitting fastq files into multiple fastq files with no more than max_fastq_records records.
Workflow run mode.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
Name of panel to use.
Exclude processes provided as a comma separated list.
Include processes that are excluded by default, provided as a comma separated list.
Manually run processes provided as a comma separated list.
Purity estimate workflow run mode.
UMI duplex delimiter as used by REDUX.
Enable REDUX UMI processing.
Which reference data types to download and extract. To be used with --mode prepare_reference.
Type of sequencing technology.
User defined target regions BED used in panel resource creation.
UMI type. Sets default '*_umi_* settings'
Reference Data options11
Name of genome reference.
Path to reference genome bwa-mem2 index.
Path to reference genome dict.
Path to reference genome FAI.
Path to reference genome FASTA.
Path to reference genome GRIDSS index.
Path to reference genome GTF.
Path to reference genome img.
Path to reference genome STAR index.
Path to HMF data.
Path to panel data.
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/oncoanalyser/blob/3.0.0/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.