https://github.com/snitkin-lab-umich/sample_snakemake
Example snakemake pipeline
https://github.com/snitkin-lab-umich/sample_snakemake
Last synced: about 2 months ago
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Example snakemake pipeline
- Host: GitHub
- URL: https://github.com/snitkin-lab-umich/sample_snakemake
- Owner: Snitkin-Lab-Umich
- Created: 2020-05-04T19:36:15.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2020-05-14T15:26:53.000Z (about 5 years ago)
- Last Synced: 2025-01-26T17:36:19.687Z (4 months ago)
- Language: R
- Size: 4.88 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Example snakemake pipeline
## Useful links
- [Snakemake documentation](https://snakemake.readthedocs.io/en/stable/)
- [Short overview](https://slides.com/johanneskoester/snakemake-short#/)
- [More detailed overview](https://slides.com/johanneskoester/snakemake-tutorial#/)
## Benefits of snakemake
- Your analysis is reproducible.
- You don't have to re-perform computationally intensive tasks early in the pipeline to change downstream analyses or figures.
- You can easily combine shell, R, python, etc. scritps into one pipeline.
- You can easily share your pipeline with others.
- You can submit a single slurm job and snakemake handles submitting the rest of your jobs for you.
## Conda
To [download miniconda](https://docs.conda.io/en/latest/miniconda.html) for linux if you don't already have it:
```
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh
```
To create and activate the conda environment:
```
conda env create -f config/env.yaml # you only have to do this once
conda activate snakemake # you have to do this every time
```
## A few basics
Useful snakemake arguments:
- `snakemake -n` dry-run (to test it out before running it)
- `snakemake` runs the pipeline
- ` snakemake --dag | dot -Tsvg > dag.svg` creates a dag (this can be super difficult to read with large complex pipelines)
## Running snakemake on the cluster
To run snakemake on the cluster, you have to modify your email address in:
- `sample.sbat`
- `config/cluster.yaml`
Then run
```
sbatch sample.sbat
```