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variantscope

somatic structural variant scoping

https://github.com/sateeshperi/variantscope

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

somatic structural variant scoping

Basic Info
  • Host: GitHub
  • Owner: sateeshperi
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 54.9 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 1
  • Open Issues: 4
  • Releases: 1
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License Citation

README.md

SowpatiLab/variantscope

Introduction

SowpatiLab/variantscope is a bioinformatics pipeline that ...

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 subject_id,sample_id,sample_type,sequence_type,filetype,filepath,indexpath subject_a,subject_a_tumor,tumor,dna,bam,assets/test-data/subject_a_tumor.dna.bwa-mem2_2.2.1.markdups.bam,assets/test-data/subject_a_tumor.dna.bwa-mem2_2.2.1.markdups.bam.bai subject_a,subject_a_normal,normal,dna,bam,assets/test-data/subject_a_normal.dna.bwa-mem2_2.2.1.markdups.bam,assets/test-data/subject_a_normal.dna.bwa-mem2_2.2.1.markdups.bam.bai

Each row represents either a tumor or normal sample for a subject, with details about the sample type, sequence type, file type, and paths to the sequence and index files.

Now, you can run the pipeline using:

bash nextflow run SowpatiLab/variantscope \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR>

[!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

SowpatiLab/variantscope was originally written by Isha Choubey.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

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

Citations

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: Sateesh_Peri
  • Login: sateeshperi
  • Kind: user
  • Location: Atlanta
  • Company: Clearnote_Health

Bioinformatics_Pipeline_Engineer

Citation (CITATIONS.md) 

# SowpatiLab/variantscope: 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

## 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
  • Issues event: 2
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  • Issue comment event: 1
  • Member event: 2
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  • Pull request review event: 25
  • Pull request review comment event: 22
  • Pull request event: 10
  • Fork event: 1
  • Create event: 10
Last Year
  • Issues event: 2
  • Delete event: 7
  • Issue comment event: 1
  • Member event: 2
  • Push event: 84
  • Pull request review event: 25
  • Pull request review comment event: 22
  • Pull request event: 10
  • Fork event: 1
  • Create event: 10

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 2
  • Total pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: 6 days
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.2
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: 6 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.2
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
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