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choleraseq

CholeraSeq pipeline

https://github.com/ceri-krisp/choleraseq

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 13 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

CholeraSeq pipeline

Basic Info
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 1
  • Open Issues: 5
  • Releases: 3
Created almost 3 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

Cite with Zenodo

Nextflow run with conda run with docker run with singularity Launch on Nextflow Tower

Introduction

CERI-KRISP/CholeraSeq is a Nextflow pipeline for data genomic analysis of Cholera outbreaks.

Reference sequence

We have created a multi-fasta reference with global cohort available on NCBI, available at the link below.

Zenodo Dataset

Documentation

The documentation for the pipeline is hosted at https://ceri-krisp.github.io/CholeraSeq/

Testing

A built-in test profile are available in the choleraseq pipeline with different size of datasets. This profile can be used to run tests on the relevant infrastructure using the test profile, to help users identify and resolve any infrastructural issue before the analysis stage.

NOTE: The snippets below assumes you have docker on the sever/machine you wish to test the pipeline. For other institutional configs please refer nf-core/configs project, which are all applicable to this pipeline.

```bash

$ nextflow run CERI-KRISP/CholeraSeq \ -profile test,docker --outdir test_output

```

For singularity please use the following command

```bash

$ nextflow run CERI-KRISP/CholeraSeq \ -profile test,singularity --outdir test_output

```

Credits

CERI-KRISP/CholeraSeq was originally written by the CholeraSeq publication authors.

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: CERI-KRISP
  • Login: CERI-KRISP
  • Kind: organization
  • Email: sanemmanueljames@gmail.com
  • Location: University of Kwazulu Natal, Nelson R. Mandela Medical School, 719 Umbilo Road, Durban, South Africa, 4001

A research and innovation sequencing platform and centre of excellence

Citation (CITATIONS.md) 

# CERI-KRISP/CholeraSeq: 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

Total
  • Create event: 5
  • Issues event: 4
  • Release event: 2
  • Issue comment event: 4
  • Push event: 98
  • Pull request event: 5
Last Year
  • Create event: 5
  • Issues event: 4
  • Release event: 2
  • Issue comment event: 4
  • Push event: 98
  • Pull request event: 5

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 3
  • Total pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 month
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.25
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 10 days
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.33
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • abhi18av (2)
  • mamunmonir (1)
Pull Request Authors
  • abhi18av (3)
  • cmavian (1)
Top Labels
Issue Labels
enhancement (2) bug (1)
Pull Request Labels

Dependencies

.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 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/fastp/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/gubbins/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/seqkit/grep/meta.yml cpan
modules/nf-core/snippy/core/meta.yml cpan
modules/nf-core/snippy/run/meta.yml cpan
pyproject.toml pypi