https://github.com/liao961120/minimal-snake
An enhanced template structure for Snakemake
https://github.com/liao961120/minimal-snake
git-bash make python reproducibility snakemake snakemake-workflow windows
Last synced: about 2 months ago
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An enhanced template structure for Snakemake
- Host: GitHub
- URL: https://github.com/liao961120/minimal-snake
- Owner: liao961120
- License: mit
- Created: 2023-02-14T06:12:50.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2023-12-15T08:54:13.000Z (over 2 years ago)
- Last Synced: 2024-01-26T22:32:18.521Z (over 2 years ago)
- Topics: git-bash, make, python, reproducibility, snakemake, snakemake-workflow, windows
- Language: HTML
- Homepage: https://yongfu.name/2023/02/15/snakemake/
- Size: 422 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
A Minimalist Workflow for Snakemake
===================================
This workflow structure is modified from Snakemake's [recommended workflow][snk-flow] with two enhancements.
1. **Simplified directory names**
`resources/` is renamed as `raw/`, and `results/` is renamed as `made/`. The
`workflow/` directory is broken down into `src/` (holding scripts) and the
`Snakefile`.
2. **Consistent relative paths**
Since `Snakefile` is now placed in the project root, the problem of
different relative paths for different directives is resolved, as long as
the user always invokes the command `snakemake -c` in the project root.
```tree
├── README.md
├── Snakefile
├── made
├── raw
└── src
```
Refer to [this post][post] for context and details.
## Usage
```bash
bash make.sh # reproduce everything (e.g., dag.png)
# snakemake -c # directly invoke snakemake command
```
[snk-flow]: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#distribution-and-reproducibility
[post]: https://yongfu.name/2023/02/15/snakemake/
---
To Do
-----
A simple command line program to take a snakemake's `--detailed-summary` table and generate a dot file of file dependency DAG. This may look like something as:
```bash
snakemake --detailed-summary -c | fileDag | dot -Tsvg -Grankdir=LR > dag.svg
```
```bash
# snakemake -c
snakemake --detatiled-summary -c # --detailed-summary outputs a TSV file
```
| output_file | date | rule | version | log-file(s) | input-file(s) | shellcmd | status | plan |
| ------------------------ | ------------------------ | ----------------- | ------- | ----------- | ---------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------- | ----------------- | --------- |
| made/wordfreq.png | Fri Dec 15 16:26:19 2023 | plot_word_freq | - | | made/merged.csv,made/stopwords.txt,src/viz.R | Rscript src/viz.R made/merged.csv made/stopwords.txt made/wordfreq.png | ok | no update |
| made/CausalModel.csv | - | extract_word_freq | - | | raw/html/CausalModel.html,raw/html/DeepLearning.html,raw/html/MultilevelModel.html,src/extract_word_freq.R | - | removed temp file | no update |
| made/DeepLearning.csv | - | extract_word_freq | - | | raw/html/CausalModel.html,raw/html/DeepLearning.html,raw/html/MultilevelModel.html,src/extract_word_freq.R | - | removed temp file | no update |
| made/MultilevelModel.csv | - | extract_word_freq | - | | raw/html/CausalModel.html,raw/html/DeepLearning.html,raw/html/MultilevelModel.html,src/extract_word_freq.R | - | removed temp file | no update |
| made/merged.csv | Fri Dec 15 16:26:15 2023 | extract_word_freq | - | | raw/html/CausalModel.html,raw/html/DeepLearning.html,raw/html/MultilevelModel.html,src/extract_word_freq.R | - | ok | no update |
| made/stopwords.txt | Fri Dec 15 16:26:12 2023 | get_stopwords | - | | src/stopwords.R | Rscript src/stopwords.R made/stopwords.txt | ok | no update |
### Some Potential Libraries
- [pydot](https://github.com/pydot/pydot)