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bactrail

Comprehensive long-term surveillance of bacterial isolates

https://github.com/idohlabs-bioinformatics/bactrail

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 10 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Comprehensive long-term surveillance of bacterial isolates

Basic Info
  • Host: GitHub
  • Owner: IDOHLabs-Bioinformatics
  • License: mit
  • Language: Nextflow
  • Default Branch: dev
  • Size: 484 KB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/bactrail

GitHub Actions CI Status GitHub Actions Linting StatusAWS CICite with Zenodo nf-test

Nextflow run with conda run with docker run with singularity Launch on Seqera Platform

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Introduction

nf-core/bactrail is a bioinformatics pipeline that ...

  1. Read QC (FastQC)
  2. Present QC for raw reads (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.

Now, you can run the pipeline using:

bash nextflow run nf-core/bactrail \ -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.

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.

Credits

nf-core/bactrail was originally written by David Schaeper.

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.

For further information or help, don't hesitate to get in touch on the Slack #bactrail channel (you can join with this invite).

Citations

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: IDOHLabs-Bioinformatics
  • Login: IDOHLabs-Bioinformatics
  • Kind: organization

Citation (CITATIONS.md) 

# nf-core/bactrail: 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/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [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.

GitHub Events

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Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v4 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/awstest.yml actions
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  • seqeralabs/action-tower-launch v2 composite
.github/workflows/branch.yml actions
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.github/workflows/ci.yml actions
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  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale 28ca1036281a5e5922ead5184a1bbf96e5fc984e composite
.github/workflows/download_pipeline.yml actions
  • actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
  • eWaterCycle/setup-singularity 931d4e31109e875b13309ae1d07c70ca8fbc8537 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/release-announcements.yml actions
  • actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
  • rzr/fediverse-action master composite
  • zentered/bluesky-post-action 80dbe0a7697de18c15ad22f4619919ceb5ccf597 composite
modules/nf-core/multiqc/meta.yml cpan
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml cpan
pyproject.toml pypi
modules/local/chewBBACA/environment.yml conda
  • chewbbaca 3.3.5.*
modules/local/fastp/environment.yml conda
  • fastp 0.23.4.*
modules/local/iqtree/environment.yml conda
  • iqtree 2.3.4.*
modules/local/panaroo/environment.yml conda
  • panaroo 1.5.0.*
modules/local/parsnp/environment.yml conda
  • parsnp 2.0.5.*
modules/local/prokka/environment.yml conda
  • prokka 1.14.6.*
modules/local/skesa/environment.yml conda
  • skesa 2.5.1.*
modules/local/snippy/environment.yml conda
  • snippy 4.6.0.*
modules/nf-core/multiqc/environment.yml conda
  • multiqc 1.21.*