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https://github.com/jdblischak/snakemake-rules
https://github.com/jdblischak/snakemake-rules
Last synced: 20 days ago
JSON representation
- Host: GitHub
- URL: https://github.com/jdblischak/snakemake-rules
- Owner: jdblischak
- Created: 2018-10-24T21:32:15.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2018-10-25T01:41:40.000Z (about 6 years ago)
- Last Synced: 2024-10-15T23:55:34.432Z (2 months ago)
- Language: Python
- Size: 6.84 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
Awesome Lists containing this project
README
---
output:
github_document:
toc: true
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = FALSE,
comment = ""
)
```
# snakemake-rules
## 1 to 1
```{bash}
bash 01/setup.sh
ls 01/fqgz
```
```{bash, include=FALSE}
snakemake -s 01/Snakefile --dag | dot -Tpng > 01/01.png
```
```{bash}
snakemake -s 01/Snakefile
```
```{bash}
ls 01/fq
```
```{bash}
snakemake -s 01/Snakefile
```
## Many to many
```{bash}
bash 02/setup.sh
ls 02/fqgz
```
```{bash, include=FALSE}
snakemake -s 02/Snakefile --dag | dot -Tpng > 02/02.png
```
```{bash}
snakemake -s 02/Snakefile
```
```{bash}
ls 02/fq
```
```{bash}
snakemake -s 02/Snakefile
```
## Many to one
```{bash}
bash 03/setup.sh
ls 03/fqgz
```
```{bash, include=FALSE}
snakemake -s 03/Snakefile --dag | dot -Tpng > 03/03.png
```
```{bash}
snakemake -s 03/Snakefile
```
```{bash}
ls 03/fq
```
```{bash}
snakemake -s 03/Snakefile
```
## Group on a known variable
```{bash}
bash 04/setup.sh
ls 04/fqgz
```
```{bash, include=FALSE}
snakemake -s 04/Snakefile --dag | dot -Tpng > 04/04.png
```
```{bash}
snakemake -s 04/Snakefile
```
```{bash}
ls 04/fq
```
```{bash}
snakemake -s 04/Snakefile
```
## Group on an unknown variable (stable input files)
```{bash}
bash 05/setup.sh
ls 05/fqgz
```
```{bash, include=FALSE}
snakemake -s 05/Snakefile --dag | dot -Tpng > 05/05.png
```
```{bash}
snakemake -s 05/Snakefile
```
```{bash}
ls 05/fq
```
```{bash}
snakemake -s 05/Snakefile
```
## Group on an unknown variable (generated input files)
```{bash}
bash 06/setup.sh
ls 06/fqgz
```
```{bash, include=FALSE}
snakemake -s 06/Snakefile --dag | dot -Tpng > 06/06.png
```
```{bash}
snakemake -s 06/Snakefile
```
```{bash}
ls 06/fq-group
```
```{bash}
snakemake -s 06/Snakefile
```