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oncoanalyser

A comprehensive cancer DNA/RNA analysis and reporting pipeline

https://github.com/nf-core/oncoanalyser

Science Score: 57.0%

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    CITATION.cff file
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    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 10 DOI reference(s) in README
  • ○
    Academic publication links
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.5%) to scientific vocabulary

Keywords

cancer clinical dna exome nextflow nf-core ngs panel pipeline rna targeted wgs wigits workflow wts
Last synced: 6 months ago · JSON representation ·

Repository

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Basic Info
Statistics
  • Stars: 80
  • Watchers: 181
  • Forks: 24
  • Open Issues: 22
  • Releases: 4
Topics
cancer clinical dna exome nextflow nf-core ngs panel pipeline rna targeted wgs wigits workflow wts
Created about 3 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/oncoanalyser

GitHub Actions CI Status GitHub Actions Linting Status AWS CI Cite with Zenodo nf-test

Nextflow nf-core template version run with conda run with docker run with singularity Launch on Seqera Platform

Get help on Slack Follow on Bluesky Follow on Mastodon Watch on YouTube

Introduction

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

  • FASTQ, BAM, and / or CRAM input files
  • WGS (whole genome sequencing), WTS (whole transcriptome sequencing), and targeted / panel sequencing1
  • Paired tumor / normal and tumor-only samples, and support for donor samples for further normal subtraction
  • Purity estimate for longitudinal samples using genomic features of the primary sample from the same patient2
  • UMI (unique molecular identifier) processing supported for DNA sequencing data
  • Most GRCh37 and GRCh38 reference genome builds

1 built-in support for the TSO500 panel with other panels and exomes requiring creation of custom panel reference data
2 for example a primary WGS tissue biospy and longitudinal low-pass WGS ccfDNA sample taken from the same patient

Pipeline overview

The pipeline mainly uses tools from WiGiTS, as well as some other external tools. There are several workflows available in oncoanalyser and the tool information below primarily relates to the wgts and targeted analysis modes.

[!NOTE] Due to the limitations of panel data, certain tools (indicated with * below) do not run in targeted mode.

For the purity_estimate mode, several of the above tools are run with adjusted configuration in addition to the following.

  • Tumor fraction estimation: WISP

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):

csv 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:

bash nextflow run nf-core/oncoanalyser \ -profile <docker/singularity/.../institute> \ -revision 2.2.0 \ --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 and is maintained by Stephen Watts (@scwatts) from 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:

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.15189386

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.

Owner

  • Name: nf-core
  • Login: nf-core
  • Kind: organization
  • Email: core@nf-co.re

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md) 

# nf-core/oncoanalyser: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [BCFtools](https://doi.org/10.1093/gigascience/giab008)

> Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2), giab008. https://doi.org/10.1093/gigascience/giab008

- [BWA](https://doi.org/10.1093/bioinformatics/btp324)

> Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760. https://doi.org/10.1093/bioinformatics/btp324

- [bwa-mem2](https://doi.org/10.1109/IPDPS.2019.00041)

> Vasimuddin, Md., Misra, S., Li, H., & Aluru, S. (2019). Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 314–324. https://doi.org/10.1109/IPDPS.2019.00041

- [CHORD](https://doi.org/10.1038/s41467-020-19406-4)

> Nguyen, L., W. M. Martens, J., Van Hoeck, A., & Cuppen, E. (2020). Pan-cancer landscape of homologous recombination deficiency. Nature Communications, 11(1), 5584. https://doi.org/10.1038/s41467-020-19406-4

- [fastp](https://doi.org/10.1093/bioinformatics/bty560)

> Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884–i890. https://doi.org/10.1093/bioinformatics/bty560

- [GATK](https://doi.org/10.1093/bioinformatics/btp324)

> McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297–1303. https://doi.org/10.1101/gr.107524.110

- [GRIDSS2](https://doi.org/10.1186/s13059-021-02423-x)

> Cameron, D. L., Baber, J., Shale, C., Valle-Inclan, J. E., Besselink, N., van Hoeck, A., Janssen, R., Cuppen, E., Priestley, P., & Papenfuss, A. T. (2021). GRIDSS2: Comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing. Genome Biology, 22(1), Article 1. https://doi.org/10.1186/s13059-021-02423-x

- [LILAC](https://doi.org/10.1038/s41588-023-01367-1)

> Martínez-Jiménez, F., Priestley, P., Shale, C., Baber, J., Rozemuller, E., & Cuppen, E. (2023). Genetic immune escape landscape in primary and metastatic cancer. Nature Genetics, 55(5), 820–831. https://doi.org/10.1038/s41588-023-01367-1

- [LINX](https://doi.org/10.1016/j.xgen.2022.100112)

> Shale, C., Cameron, D. L., Baber, J., Wong, M., Cowley, M. J., Papenfuss, A. T., Cuppen, E., & Priestley, P. (2022). Unscrambling cancer genomes via integrated analysis of structural variation and copy number. Cell Genomics, 2(4). https://doi.org/10.1016/j.xgen.2022.100112

- [PURPLE](https://doi.org/10.1038/s41586-019-1689-y)

> Priestley, P., Baber, J., Lolkema, M. P., Steeghs, N., de Bruijn, E., Shale, C., Duyvesteyn, K., Haidari, S., van Hoeck, A., Onstenk, W., Roepman, P., Voda, M., Bloemendal, H. J., Tjan-Heijnen, V. C. G., van Herpen, C. M. L., Labots, M., Witteveen, P. O., Smit, E. F., Sleijfer, S., … Cuppen, E. (2019). Pan-cancer whole-genome analyses of metastatic solid tumours. Nature, 575(7781), 210–216. https://doi.org/10.1038/s41586-019-1689-y

- [Sambamba](https://doi.org/10.1093/bioinformatics/btv098)

> Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J., & Prins, P. (2015). Sambamba: Fast processing of NGS alignment formats. Bioinformatics, 31(12), 2032–2034. https://doi.org/10.1093/bioinformatics/btv098

- [SAMtools](https://doi.org/10.1093/gigascience/giab008)

> Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2), giab008. https://doi.org/10.1093/gigascience/giab008

- [STAR](https://doi.org/10.1093/bioinformatics/bts635)

> Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013). STAR: Ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15–21. https://doi.org/10.1093/bioinformatics/bts635

- [VIRUSBreakend](https://doi.org/10.1093/bioinformatics/btab343)

> Cameron, D. L., Jacobs, N., Roepman, P., Priestley, P., Cuppen, E., & Papenfuss, A. T. (2021). VIRUSBreakend: Viral Integration Recognition Using Single Breakends. Bioinformatics, 37(19), 3115–3119. https://doi.org/10.1093/bioinformatics/btab343

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

> Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

> Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

> da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

> Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total
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  • Commit comment event: 6
  • Release event: 2
  • Issues event: 90
  • Watch event: 35
  • Delete event: 140
  • Issue comment event: 298
  • Push event: 444
  • Pull request review comment event: 40
  • Pull request review event: 109
  • Pull request event: 151
  • Fork event: 14
Last Year
  • Create event: 163
  • Commit comment event: 6
  • Release event: 2
  • Issues event: 90
  • Watch event: 35
  • Delete event: 140
  • Issue comment event: 298
  • Push event: 444
  • Pull request review comment event: 40
  • Pull request review event: 109
  • Pull request event: 151
  • Fork event: 14

Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v3 composite
  • nf-core/tower-action v3 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v3 composite
  • nf-core/tower-action v3 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v2 composite
.github/workflows/linting.yml actions
  • actions/checkout v2 composite
  • actions/setup-node v2 composite
  • actions/setup-python v3 composite
  • actions/upload-artifact v2 composite
  • mshick/add-pr-comment v1 composite
  • nf-core/setup-nextflow v1 composite
  • psf/black stable composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
pyproject.toml pypi