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bgcflow_wrapper

A snakemake wrapper and utility tools command line interface for BGCFlow.

https://github.com/nbchub/bgcflow_wrapper

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
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.9%) to scientific vocabulary
Last synced: 9 months ago · JSON representation ·

Repository

A snakemake wrapper and utility tools command line interface for BGCFlow.

Basic Info
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 1
  • Open Issues: 5
  • Releases: 16
Created over 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Citation Authors

README.md

BGCFlow Wrapper

Release Status CI Status Documentation Status

A snakemake wrapper and utility tools for BGCFlow, a systematic workflow for the analysis of biosynthetic gene clusters across large genomic datasets.

For more details, see documentation.

Please refer to the BGCFlow WIKI for detailed examples and use cases:

wiki

Publication

Matin Nuhamunada, Omkar S Mohite, Patrick V Phaneuf, Bernhard O Palsson, Tilmann Weber, BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets, Nucleic Acids Research, 2024;, gkae314, https://doi.org/10.1093/nar/gkae314

Setup

Setup via Conda

To install bgcflow_wrapper with conda/mamba, run this command in your terminal:

```bash

create and activate new conda environment

mamba create -n bgcflow -c conda-forge python=3.11 pip openjdk -y conda activate bgcflow

install BGCFlow wrapper

pip install bgcflow_wrapper ```

Features

function

```bash

$ bgcflow

Usage: bgcflow [OPTIONS] COMMAND [ARGS]...

A snakemake wrapper and utility tools for BGCFlow (https://github.com/NBChub/bgcflow)

Options: --version Show the version and exit. -h, --help Show this message and exit.

Commands: build Build Markdown report or use dbt to build DuckDB database. clone Get a clone of BGCFlow to local directory. deploy [EXPERIMENTAL] Deploy BGCFlow locally using snakedeploy. get-result View a tree of a project results or get a copy using Rsync. init Create projects or initiate BGCFlow config from template. pipelines Get description of available pipelines from BGCFlow. run A snakemake CLI wrapper to run BGCFlow. serve Serve static HTML report or other utilities (Metabase, etc.). sync Upload and sync DuckDB database to Metabase. ```

Credits

This package was created with the ppw tool. For more information, please visit the project page.

Owner

  • Name: NBCHub
  • Login: NBChub
  • Kind: organization
  • Location: Denmark

Repositories for analyzing large scale datasets for natural products discovery developed at DTU Biosustain

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you find this repository useful, please cite it using the following publication."
authors:
- family-names: "Nuhamunada"
  given-names: "Matin"
  orcid: "https://orcid.org/0000-0003-3177-8299"
- family-names: "Mohite"
  given-names: "Omkar S."
  orcid: "https://orcid.org/0000-0002-3240-1656"
- family-names: "Phaneuf"
  given-names: "Patrick V."
  orcid: "https://orcid.org/0000-0002-4122-6589"
- family-names: "Palsson"
  given-names: "Bernhard O."
  orcid: "https://orcid.org/0000-0003-2357-6785"
- family-names: "Weber"
  given-names: "Tilmann"
  orcid: "https://orcid.org/0000-0002-8260-5120"
title: "bgcflow_wrapper"
version: 0.4.0
doi: "N/A"
date-released: 2023-06-15
url: "https://github.com/NBChub/bgcflow_wrapper"
preferred-citation:
  type: article
  authors:
  - family-names: "Nuhamunada"
    given-names: "Matin"
    orcid: "https://orcid.org/0000-0003-3177-8299"
  - family-names: "Mohite"
    given-names: "Omkar S."
    orcid: "https://orcid.org/0000-0002-3240-1656"
  - family-names: "Phaneuf"
    given-names: "Patrick V."
    orcid: "https://orcid.org/0000-0002-4122-6589"
  - family-names: "Palsson"
    given-names: "Bernhard O."
    orcid: "https://orcid.org/0000-0003-2357-6785"
  - family-names: "Weber"
    given-names: "Tilmann"
    orcid: "https://orcid.org/0000-0002-8260-5120"
  doi: "10.1093/nar/gkae314"
  journal: "Nucleic Acids Research"
  publisher: "Oxford University Press"
  title: "BGCFlow: Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets"
  year: 2024
  url: "https://doi.org/10.1093/nar/gkae314"

GitHub Events

Total
  • Release event: 1
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 2
  • Push event: 21
  • Pull request event: 6
  • Fork event: 1
  • Create event: 5
Last Year
  • Release event: 1
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 2
  • Push event: 21
  • Pull request event: 6
  • Fork event: 1
  • Create event: 5

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 9
  • Total pull requests: 38
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 5 days
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 0.11
  • Average comments per pull request: 0.24
  • Merged pull requests: 29
  • Bot issues: 0
  • Bot pull requests: 15
Past Year
  • Issues: 1
  • Pull requests: 8
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 minutes
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.5
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 4
View more stats
Top Authors
Issue Authors
  • matinnuhamunada (8)
  • OmkarSaMo (1)
Pull Request Authors
  • matinnuhamunada (22)
  • dependabot[bot] (15)
  • OmkarSaMo (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (15)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 88 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
pypi.org: bgcflow_wrapper

A snakemake wrapper and utility tools command line interface for BGCFlow.

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 88 Last month
Rankings
Dependent packages count: 7.3%
Stargazers count: 27.9%
Forks count: 29.9%
Average: 33.4%
Dependent repos count: 68.4%
Maintainers (1)
matinnu
Last synced: 10 months ago

Dependencies

poetry.lock pypi
  • 162 dependencies
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