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scnapattern

A workflow to calculate SCNA patterns as described in Pesenti et al.

https://github.com/dincalcilab/scnapattern

Science Score: 44.0%

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Repository

A workflow to calculate SCNA patterns as described in Pesenti et al.

Basic Info
  • Host: GitHub
  • Owner: DIncalciLab
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Size: 203 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created over 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

Somatic copy number alteration (SCNA) pattern identification in shallow whole-genome sequencing data

Introduction

dincalcilab/scnapattern is a bioinformatics pipeline that assigns somatic copy number alterations (SCNA) patterns (S, stable; U, unstable; HU, highly unstable) as described in Copy number alterations in stage I epithelial ovarian cancer highlight three genomic patterns associated with prognosis by Pesenti, Beltrame, et al.

This pipeline requires shallow whole-genome sequencing (sWGS) data with absolute copy number and ploidy estimates. Currently segmentation outputs from ASCAT.sc, ACE, and ichorCNA are supported natively.

The pipeline includes these steps:

  1. Calculate SCNA patterns for given inputs
  2. Output a table with patterns and parameters for each analyzed sample
  3. Generate a QC summary (MultiQC)

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.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

csv sample,filename,ploidy,format Sample_1,Sample1.cna.seg,2,ichorcna

Each row represents a sample name, the associated absolute path to the segment file, the ploidy of the sample, and the data format (either ascat, ace, or ichorcna).

Now, you can run the pipeline using:

bash nextflow run dincalcilab/scnapattern \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR> \ --genome <GENOME> \ --genomestyle <GENOMESTYLE>

Where GENOME is either hg19 or hg38 and genomestyle is either ucsc (chr prefix for chomosomes) or ncbi (no chr prefix). Note that you must use a Nextflow configuration profile that supports Docker or Singularity images, as some tools are only provided by containers.

[!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.

Credits

dincalcilab/scnapattern was originally written by Luca Beltrame (@lbeltrame).

Contributions and Support

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

Citations

If you use dincalcilab/scnapattern for your analysis, please cite it using the following doi: 10.1016/j.ejca.2022.05.005

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

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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: DIncalciLab
  • Login: DIncalciLab
  • Kind: organization
  • Location: Italy

Citation (CITATIONS.md) 

# dincalcilab/scnapattern: Citations

## [Pattern calling algorithm](https://pubmed.ncbi.nlm.nih.gov/35714451/)

> Pesenti C, Beltrame L, Velle A, Fruscio R, Jaconi M, Borella F, Cribiù FM, Calura E, Venturini LV, Lenoci D, Agostinis F, Katsaros D, Panini N, Bianchi T, Landoni F, Miozzo M, D'Incalci M, Brenton JD, Romualdi C, Marchini S. Copy number alterations in stage I epithelial ovarian cancer highlight three genomic patterns associated with prognosis. Eur J Cancer. 2022 Aug;171:85-95. doi: 10.1016/j.ejca.2022.05.005. PMID: 35714451.

## [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

-- [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)

  > 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.

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Dependencies

modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/local/scnapattern/environment.yaml pypi
modules/nf-core/custom/dumpsoftwareversions/environment.yml pypi
modules/nf-core/multiqc/environment.yml pypi
pyproject.toml pypi