https://github.com/ctubbs750/snakemake-workflow-template

Project structure and template for use in a Snakemake workflow.
https://github.com/ctubbs750/snakemake-workflow-template

python shell-scripting snakemake template

Last synced: about 1 year ago
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Project structure and template for use in a Snakemake workflow.

• Host: GitHub
• URL: https://github.com/ctubbs750/snakemake-workflow-template
• Owner: ctubbs750
• Created: 2024-09-17T02:31:23.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2025-04-06T20:49:22.000Z (about 1 year ago)
• Last Synced: 2025-04-30T22:55:39.400Z (about 1 year ago)
• Topics: python, shell-scripting, snakemake, template
• Language: Python
• Homepage:
• Size: 6.84 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# snakemake-workflow-template

snakemake-workflow-template provides a generic project template for use in Snakemake workflows. This structure is derived from the recommended Snakemake directory structure ([here](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html)), with a few modifications to make that I found more compatible with research and work conducted on high-performance compute (HPC) clusters.

### Usage

To use this template you can select `Use this template` from the repo home page. Alternatively, you clone it through the web url followed by a few commands to clean things up:

```

$ git clone [repo web url]

$ mv snakemake-workflow-template/ [workflow-name]

$ cd [workflow-name]

$ find . -type f -name "*.gitignore" -exec rm -f {} +

```