nf-core pipeline · cancer, clinical, ctdna
nf-core/oncoanalyser
A Nextflow pipeline for analysing and reporting cancer DNA and RNA sequencing data using the WiGiTS toolkit.
What nf-core/oncoanalyser is
nf-core/oncoanalyser is a Nextflow bioinformatics pipeline developed for comprehensive cancer DNA and RNA sequencing analysis and reporting. Written and maintained by Stephen Watts from the Genomics Platform Group at the University of Melbourne Centre for Cancer Research, with assistance from the Hartwig Medical Foundation Australia and Oliver Hofmann, the pipeline wraps the Hartwig Medical Foundation WiGiTS toolkit along with external sequencing tools into reproducible workflows.
The pipeline enables researchers and clinicians to process tumour sequencing data across multiple experimental designs. It accepts whole-genome sequencing (WGS), whole-transcriptome sequencing (WTS), and targeted or panel sequencing datasets, supporting paired tumour-normal, tumour-only, and donor-subtracted comparisons.
To support operational requirements and accreditation standards in clinical settings, nominated stable feature releases receive extended support, including bug and security patches on dedicated long-lived branches.
What the pipeline does
The pipeline takes FASTQ, BAM, or CRAM inputs mapped to GRCh37 or GRCh38 reference genomes, including DNA data with unique molecular identifiers (UMIs). Sequence alignment is performed using BWA-MEM2 for DNA and STAR for RNA, followed by read post-processing using REDUX for DNA and Picard MarkDuplicates for RNA. Small variant calling (single-nucleotide variants, multi-nucleotide variants, and indels) is conducted by SAGE and annotated with PAVE, while ESVEE calls structural variants (SVs), and AMBER, COBALT, and PURPLE resolve copy number variants (CNVs) and tumour purity.
Downstream modules interpret genomic alterations and integrate multi-omic measurements. LINX interprets structural variants and driver events, ISOFOX analyses RNA transcripts, and Qsee computes sequencing quality control metrics. Immune characteristics are assessed using LILAC, CIDER, and NEO, alongside PEACH for pharmacogenomics. In whole-genome modes, VIRUSbreakend and VirusInterpreter identify oncoviruses, TEAL characterises telomeres, SIGS fits mutational signatures, CHORD predicts homologous recombination deficiency (HRD), and CUPPA predicts tumour tissue of origin. Longitudinal monitoring in purity estimate mode uses WISP to calculate tumour fractions, and final summary reports are compiled by ORANGE and linxreport.
Key facts
- Pipeline framework
- Nextflow (nf-core)
- Core toolkit
- Hartwig Medical Foundation WiGiTS
- Latest release
- 3.0.0
- Supported inputs
- FASTQ, BAM, CRAM
- Sequencing modalities
- WGS, WTS, targeted panel sequencing
- Reference genomes
- Most GRCh37 and GRCh38 builds
- Primary maintainer
- Stephen Watts (University of Melbourne Centre for Cancer Research)
What you can use it for
- Comprehensive whole-genome and transcriptome cancer profiling
- Processing matched tumour and normal WGS alongside tumour WTS to identify somatic mutations, structural variations, copy number changes, gene fusions, and transcript features.
- Targeted oncology panel analysis
- Analysing panel data, such as Illumina TruSight Oncology 500 (TSO500) or custom panels, for diagnostic variant calling, immune markers, and pharmacogenomics.
- Longitudinal liquid biopsy monitoring
- Estimating tumour fraction and purity in longitudinal samples, such as low-pass WGS circulating cell-free DNA (ccfDNA), using baseline features from a patient's primary biopsy.
- Genomic scar and signature interpretation
- Evaluating mutational signatures with SIGS and homologous recombination deficiency (HRD) using CHORD on whole-genome tumour data.
- Oncoviral and tissue-of-origin characterisation
- Detecting viral integrations via VIRUSbreakend and VirusInterpreter and predicting primary tissue of origin with CUPPA in whole-genome analyses.
Run it here
The research agent runs nf-core/oncoanalyser with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Unifies DNA and RNA somatic analysis, variant calling, driver interpretation, and reporting in a single pipeline.
- Supports multiple input types, including paired tumour-normal, tumour-only, and donor-subtracted samples.
- Incorporates unique molecular identifier (UMI) processing for DNA sequencing libraries.
- Maintains extended-support stable branches to meet long-term operational and clinical accreditation requirements.
Watch out for
- Several tools—including VIRUSbreakend, VirusInterpreter, TEAL, NEO, SIGS, CHORD, and CUPPA—cannot run in targeted panel mode.
- Panel analysis requires custom reference data preparation for any assay other than the built-in TruSight Oncology 500 (TSO500) panel.
- Pipeline parameters cannot be supplied via custom configuration files using the Nextflow -c option and must be provided through the command line or parameter files.
Questions
Can I run nf-core/oncoanalyser without my own cluster?
The research agent runs nf-core/oncoanalyser with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/oncoanalyser under?
MIT, like every nf-core pipeline.
What input file formats does oncoanalyser accept?
The pipeline accepts FASTQ, BAM, and CRAM formats for DNA and RNA sequencing.
Can oncoanalyser run without a matched normal sample?
Yes, the pipeline supports tumour-only analysis as well as paired tumour-normal designs and donor samples for normal subtraction.
Which targeted panels are supported out of the box?
The pipeline includes built-in reference support for the Illumina TruSight Oncology 500 (TSO500) panel, while other panels and exomes require users to generate custom panel reference data.
How does the pipeline handle longitudinal samples?
In purity estimate mode, the pipeline uses WISP and primary tumour genomic features to estimate tumour fraction in longitudinal samples, such as low-pass WGS ccfDNA.
Which reference genome builds are supported?
The pipeline supports most GRCh37 and GRCh38 reference genome builds.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/oncoanalyser's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.