https://github.com/ggonnella/snacli
Simplify writing dual use scripts for CLI and Snakemake
https://github.com/ggonnella/snacli
Last synced: 3 months ago
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Simplify writing dual use scripts for CLI and Snakemake
- Host: GitHub
- URL: https://github.com/ggonnella/snacli
- Owner: ggonnella
- License: other
- Created: 2022-04-08T13:40:04.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2022-07-13T16:54:45.000Z (almost 3 years ago)
- Last Synced: 2024-04-25T06:43:22.079Z (about 1 year ago)
- Language: Python
- Size: 27.3 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.txt
- License: LICENSE.txt
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README
# SnaCLI
SnaCLI is a library which simplifies writing scripts which can be both run
directly from the command line (based on docopt), as well as be called in a
Snakemake file.
## Introduction
In the _Snakemake_ workflow management system, tasks can call Python scripts
and pass them input, output and log filenames as well as global configuration
values and non-filename parameters.
The system for passing and accessing these arguments is different to that
adopted by command line tools (for example using the _docopt_ library).
SnaCLI allows to easily combine the two approaches (docopt and snakemake) for
providing arguments to a script. Script based on SnaCLI can be invoked both from
the command line and from snakemake. Inside the script, the
same code can be used in both cases, without modifications.
## Usage
The usage of the library is explained in the
[user manual](https://github.com/ggonnella/snacli/blob/main/docs/usage.md).