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odhl_ar

ODHL AR Pipeline

https://github.com/odhl/odhl_ar

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
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    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 (7.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

ODHL AR Pipeline

Basic Info
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

rAcecaR: Antimicrobial Resistance (AR) Bioinformatics Pipeline

Hits

Warning
The results generated by this pipeline are not CLIA certified and should not be considered diagnostic.

Introduction

The ODHL_rAcecaR pipeline is designed for the detection and characterization of antimicrobial resistance (AMR) genes and other relevant genomic features from high-throughput sequencing data. This pipeline processes bacterial whole genome sequencing (WGS) and metagenomic sequencing data to identify antimicrobial resistance determinants, sequence types, and genomic features relevant to public health surveillance and epidemiological investigations.

This workflow is developed and maintained by the Ohio Department of Health Laboratory (ODHL) and is built using Nextflow, a robust workflow management system that ensures reproducibility and scalability across HPC clusters, cloud environments, and local machines. The pipeline was built off the work of the CDC Phoenix Pipeline. The workflow leverages Docker and Singularity containers to provide a standardized execution environment. Nextflow

Pipeline Information

View our docs website for more information on the pipeline, how to execute, input requirements, output files, and contributions.

Owner

  • Name: ODHL
  • Login: ODHL
  • Kind: organization

GitHub Events

Total
  • Delete event: 1
  • Public event: 1
  • Push event: 29
  • Create event: 1
Last Year
  • Delete event: 1
  • Public event: 1
  • Push event: 29
  • Create event: 1

Dependencies

.github/workflows/awsfulltest.yml actions
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.github/workflows/awstest.yml actions
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.github/workflows/branch.yml actions
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.github/workflows/build_mkdocs.yaml actions
  • actions/checkout v4 composite
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.github/workflows/ci.yml actions
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  • eWaterCycle/setup-apptainer main composite
  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v2 composite
.github/workflows/clean-up.yml actions
  • actions/stale 28ca1036281a5e5922ead5184a1bbf96e5fc984e composite
.github/workflows/download_pipeline.yml actions
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  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v2 composite
.github/workflows/fix-linting.yml actions
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.github/workflows/linting.yml actions
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.github/workflows/linting_comment.yml actions
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.github/workflows/release-announcements.yml actions
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.github/workflows/template_version_comment.yml actions
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