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sash

https://github.com/umccr/sash

Science Score: 44.0%

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Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: umccr
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 2.51 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 7
  • Releases: 0
Created almost 3 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License Citation

README.md

sash

sash is the UMCCR post-processing WGS workflow. The workflow takes DRAGEN small variant calls and oncoanalyser results as input to perform annotation, prioritisation, rescue and filtering, and reporting for the WGS variant data. Additionally, sash runs several sensors for biomarker assessment and genomic characterisation including HRD status, mutational signatures, purity/ploidy, MSI, and TMB.

While the sash workflow utilises a range of tools and software, it is most closely coupled with bolt, a Python package that implements the UMCCR post-processing logic and supporting functionality.

Table of contents

Summary

The general processes sash runs include:

  • gpgr for generating the summary Cancer Report
  • PCGR to report processed small somatic variants (annotated, rescued, filtered, prioritised)
  • CPSR to report processed small germline variants (filtered, annotated, prioritised)
  • linxreport to collate SV annotations and plots from LINX
  • MultiQC for reporting various WGS statistics / metrics for QC
  • SAGE variant calling to supplement DRAGEN small somatic variants
  • PURPLE for TMB, MSI, CNV calling, and purity / ploidy estimation
  • HRDetect and CHORD for HRD inference
  • MutationalPatterns to fit mutational signatures

Requirements

  • Java
  • Nextflow ≥22.10.6
  • Docker

Usage

Create a samplesheet

text id,subject_name,sample_name,filetype,filepath subject_a.example,subject_a,sample_germline,dragen_germline_dir,/path/to/dragen_germline/ subject_a.example,subject_a,sample_somatic,dragen_somatic_dir,/path/to/dragen_somatic/ subject_a.example,subject_a,sample_somatic,oncoanalyser_dir,/path/to/oncoanalyser/

Execute analysis

bash nextflow run scwatts/sash \ -profile docker \ --input samplesheet.csv \ --ref_data_path /path/to/reference_data/ \ --outdir output/

Owner

  • Name: UMCCR
  • Login: umccr
  • Kind: organization
  • Email: oliver.hofmann@unimelb.edu.au
  • Location: Melbourne, Australia

University of Melbourne Centre for Cancer Research

Citation (CITATIONS.md) 

# umccr/sash: 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

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## 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)

- [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

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Last Year
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