https://github.com/bactopia/nf-bactopia
A Nextflow plugin for Bactopia
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.1%) to scientific vocabulary
Repository
A Nextflow plugin for Bactopia
Basic Info
- Host: GitHub
- Owner: bactopia
- License: apache-2.0
- Language: Groovy
- Default Branch: main
- Size: 248 KB
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
nf-bactopia
A Nextflow plugin for specifically for usage with Bactopia. It based of the modified nf-core libs and the nf-schema plugin.
This plugin will replicate the functionality of the previous libraries, while being compatible with future releases of Nextflow (>= 25).
Again, while you are free to do what you want, this plugin is specifically designed for Bactopia and will likely not work with other pipelines.
Setting up a Development Environment
Clone the repository
```{bash} git clone git@github.com:bactopia/nf-bactopia.git
cd nf-bactopia ```
Create a new conda environment
{bash}
conda create -y -n nf-bactopia \
-c conda-forge \
-c bioconda \
make \
'nextflow>=25'
conda activate nf-bactopia
Build the plugin and install
{bash}
make assemble
make install
Use the plugin
The make install should put the plugin in your ~/.nextflow/plugins directory. So it should
just work!
{bash}
NXF_VER=25.06.0-edge nextflow run ...
Owner
- Name: Bactopia
- Login: bactopia
- Kind: organization
- Location: United States of America
- Website: https://bactopia.github.io/
- Twitter: rpetit3
- Repositories: 4
- Profile: https://github.com/bactopia
Nextflow DSL2 pipeline for the complete analysis of bacterial genomes
GitHub Events
Total
- Push event: 9
- Create event: 2
Last Year
- Push event: 9
- Create event: 2