Introduction

nf-core/oncoanalyser is a Nextflow implementation of the comprehensive cancer DNA and RNA analysis and reporting workflow from the Hartwig Medical Foundation. For detailed information on each component of the Hartwig Medical Foundation workflow, please refer to hartwigmedical/hmftools.

The oncoanalyser pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website.

Pipeline summary

The following processes and tools can be run with oncoanalyser:

• SNV and MNV calling (SAGE, PAVE)
• SV calling (SV Prep, GRIDSS, GRIPSS, PURPLE, LINX)
• CNV calling (AMBER, COBALT, PURPLE)
• Transcript analysis (Isofox)
• Oncoviral detection (VIRUSBreakend, Virus Interpreter)
• HLA calling (LILAC)
• HRD status prediction (CHORD)
• Mutational signature fitting (Sigs)
• Tissue of origin prediction (CUPPA)
• Report generation (ORANGE, linxreport)

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Create a samplesheet containing your inputs:

group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
P1__wgts,P1,SA,tumor,dna,bam,/path/to/SA.tumor.dna.wgs.bam
P1__wgts,P1,SB,tumor,rna,bam,/path/to/SB.tumor.rna.wts.bam
P1__wgts,P1,SC,normal,dna,bam,/path/to/SC.normal.dna.wgs.bam

Launch oncoanalyser:

nextflow run nf-core/oncoanalyser \
   -revision v0.3.1 \
   -profile docker \
   --mode wgts \
   --genome GRCh38_hmf \
   --input samplesheet.csv \
   --outdir output/

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Version support

As oncoanalyser is used in clinical settings and is subject to accreditation standards in some instances, there is a need for long-term stability and reliability for feature releases in order to meet operational requirements. This is accomplished through long-term support of several nominated feature releases, which all receive bug fixes and security fixes during the period of extended support.

Each release that is given extended support is allocated a separate long-lived git branch with the 'stable' prefix, e.g. stable/1.2.x, stable/1.5.x. Feature development otherwise occurs on the main branch.

Credits

The oncoanalyser pipeline was written by Stephen Watts while in the Genomics Platform Group at the University of Melbourne Centre for Cancer Research.

We thank the following organisations and people for their extensive assistance in the development of this pipeline, listed in alphabetical order:

• Hartwig Medical Foundation Australia
• Oliver Hofmann

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #oncoanalyser channel (you can join with this invite).

Citations

You can cite the oncoanalyser zenodo record for a specific version using the following doi: 10.5281/zenodo.XXXXXXX

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.