Introduction

nf-core/oncoanalyser is a Nextflow pipeline for the comprehensive analysis of cancer genomes and transcriptomes using the WiGiTS toolkit from the Hartwig Medical Foundation. The pipeline supports a wide range of experimental setups:

• FASTQ, BAM, or CRAM input files
• WGS (whole genome sequencing), WTS (whole transcriptome sequencing), and targeted / panel sequencing (built-in support for the TSO500 panel with other panels and exome requiring panel reference data generation)
• Paired tumor / normal and tumor-only sample setups, donor sample support for further normal subtraction (e.g. for patients with bone marrow transplants or other contaminants in the tumor)
• UMI (unique molecular identifier) processing supported for DNA sequencing data
• Most GRCh37 and GRCh38 reference genome builds

Pipeline overview

The pipeline mainly uses tools from WiGiTS, as well as some external tools. Due to the limitations of panel data, certain tools (indicated with * below) do not run in targeted mode.

• Read alignment: BWA-MEM2 (DNA), STAR (RNA)
• Read post-processing: REDUX (DNA), Picard MarkDuplicates (RNA)
• SNV, MNV, INDEL calling: SAGE, PAVE
• SV calling: ESVEE
• CNV calling: AMBER, COBALT, PURPLE
• SV and driver event interpretation: LINX
• RNA transcript analysis: ISOFOX
• Oncoviral detection: VIRUSbreakend*, VirusInterpreter*
• Immune analysis: LILAC, NEO*
• Mutational signature fitting: SIGS*
• HRD prediction: CHORD*
• Tissue of origin prediction: CUPPA*
• Summary report: 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 with your inputs (WGS/WTS BAMs in this example):

group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1_WGTS,PATIENT1,PATIENT1-N,normal,dna,bam,/path/to/PATIENT1-N.dna.bam
PATIENT1_WGTS,PATIENT1,PATIENT1-T,tumor,dna,bam,/path/to/PATIENT1-T.dna.bam
PATIENT1_WGTS,PATIENT1,PATIENT1-T-RNA,tumor,rna,bam,/path/to/PATIENT1-T.rna.bam

Launch oncoanalyser:

nextflow run nf-core/oncoanalyser \
  -profile <docker|singularity|...> \
  -revision 2.0.0 \
  --mode <wgts|targeted> \
  --genome <GRCh37_hmf|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 information

Extended support

As oncoanalyser is used in clinical settings and 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 dev branch with stable releases pushed to master.

Versions nominated to have current long-term support:

• TBD

Known issues

Please refer to this page for details regarding any known issues.

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.