https://github.com/clavellab/template-dereplication-workflow

Workflow template to dereplicate and cherry-pick mass spectrometry spectra
https://github.com/clavellab/template-dereplication-workflow

Last synced: about 1 month ago
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Workflow template to dereplicate and cherry-pick mass spectrometry spectra

• Host: GitHub
• URL: https://github.com/clavellab/template-dereplication-workflow
• Owner: ClavelLab
• License: gpl-3.0
• Created: 2023-10-27T14:41:39.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2024-11-12T16:22:26.000Z (about 2 months ago)
• Last Synced: 2024-11-12T16:43:52.978Z (about 2 months ago)
• Language: R
• Size: 61.5 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        

# template-dereplication-workflow

[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)

`template-dereplication-workflow` provides a reusable template to run a reproducible workflow (using [`{targets}`](https://docs.ropensci.org/targets/)) to dereplicate and cherry-pick mass spectrometry spectra using the [`{maldipickr}`](https://cran.r-project.org/package=maldipickr), in order to reduce the redundancy of bacterial isolates.

 

## Usage

1. Clone the repository

2. Set up the dependencies using `renv::restore()`

3. Fill out the needed parameters in `_targets.R`

4. Evaluate the workflow using `targets::tar_manifest()`

5. Run the workflow with `targets::tar_make()`