https://github.com/snakemake/snakemake-github-action
A Github action for running a Snakemake workflow
https://github.com/snakemake/snakemake-github-action
Last synced: about 1 year ago
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A Github action for running a Snakemake workflow
- Host: GitHub
- URL: https://github.com/snakemake/snakemake-github-action
- Owner: snakemake
- License: mit
- Created: 2019-10-14T13:26:29.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2023-08-15T11:36:48.000Z (almost 3 years ago)
- Last Synced: 2024-04-25T17:41:54.750Z (about 2 years ago)
- Language: Shell
- Size: 49.8 KB
- Stars: 51
- Watchers: 3
- Forks: 11
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# Snakemake github action
This action runs Snakemake on the repository.
## Inputs
### `directory`
**Required** The working directory to use. Default `.test`.
### `snakefile`
The Snakefile containing the workflow description. Default `Snakefile`.
### `args`
Additional arguments to pass to Snakemake.
### `stagein`
Preliminary commands to run before the workflow execution.
### `task`
Whether to run Snakemake or to generate a container image specification (in the form of a Dockerfile) that contains all required environments. Can be either `run` or `containerize`. Default `run`.
### `show-disk-usage-on-error`
Whether used disk space shall be printed if Snakemake fails. Can be either `true` or `false` (default: `false`).
## Example usage
```yaml
- name: Linting
uses: snakemake/snakemake-github-action@v1
with:
directory: '.test'
snakefile: 'workflow/Snakefile'
args: '--lint'
- name: Testing
uses: snakemake/snakemake-github-action@v1
with:
directory: '.test'
snakefile: 'workflow/Snakefile'
args: '--cores 1 --use-conda --conda-cleanup-pkgs cache'
stagein: '' # additional preliminary commands to run (can be multiline)
show-disk-usage-on-error: true
- name: Create container file
uses: snakemake/snakemake-github-action@v1
with:
snakefile: 'workflow/Snakefile'
task: 'containerize'
```