https://github.com/ctb/2018-snakemake-cli
https://github.com/ctb/2018-snakemake-cli
Last synced: 9 months ago
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- Host: GitHub
- URL: https://github.com/ctb/2018-snakemake-cli
- Owner: ctb
- Created: 2018-03-17T03:47:01.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2019-01-28T19:35:28.000Z (over 7 years ago)
- Last Synced: 2025-07-29T10:57:31.060Z (11 months ago)
- Language: Python
- Size: 1.95 KB
- Stars: 4
- Watchers: 1
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 2018-snakemake-cli
An example of parameterizing snakemake workflows with a simple CLI.
Usage:
```
./run
```
e.g.
```
rm -f hello.txt
./run workflow-hello params-amy
```
creates `hello.txt` with "hello amy" in it, while
```
rm -f hello.txt
./run workflow-hello params-beth
```
creates `hello.txt` with "hello beth" in it.
Here, the workflow file `workflow-hello.json` specifes the target
`hello.txt`, while the parameters file `params-amy` parameterizes
the workflow with the name "amy".
Likewise,
```
rm -f goodbye.txt
./run workflow-goodbye params-beth
```
will put `goodbye beth` in `goodbye.txt`.
All workflows use the same set of Snakemake rules in `Snakefile`.
See also: https://github.com/charlesreid1/2019-snakemake-cli