https://github.com/silask/abinner
https://github.com/silask/abinner
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/silask/abinner
- Owner: SilasK
- License: mit
- Created: 2018-07-20T07:35:36.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2018-07-20T08:40:06.000Z (almost 7 years ago)
- Last Synced: 2025-01-21T20:48:38.969Z (5 months ago)
- Language: Python
- Size: 7.81 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Snakemake workflow: ABinner
[](https://snakemake.bitbucket.io)
[](https://travis-ci.org/snakemake-workflows/abinner)This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose and domain.
Insert your code into the respective folders, i.e. `scripts`, `rules`, and `envs`. Define the entry point of the workflow in the `Snakefile` and the main configuration in the `config.yaml` file.## Authors
* Silas Kieser (@silask)
## Usage
### Step 1: Install workflow
If you simply want to use this workflow, download and extract the [latest release](https://github.com/snakemake-workflows/abinner/releases).
If you intend to modify and further develop this workflow, fork this repository. Please consider providing any generally applicable modifications via a pull request.In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).
### Step 2: Configure workflow
Configure the workflow according to your needs via editing the file `config.yaml`.
### Step 3: Execute workflow
Test your configuration by performing a dry-run via
snakemake -n
Execute the workflow locally via
snakemake --cores $N
using `$N` cores or run it in a cluster environment via
snakemake --cluster qsub --jobs 100
or
snakemake --drmaa --jobs 100
See the [Snakemake documentation](https://snakemake.readthedocs.io) for further details.
## Testing
Tests cases are in the subfolder `.test`. They should be executed via continuous integration with Travis CI.