README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# mothur-snakemake-workflow <img src='figures/mothur-snakemake-workflow.png' align="right" height="139" />

This example workflow implements the MiSeq SOP as a reproducible Snakemake workflow

<!-- badges: start -->
[![build](https://github.com/SchlossLab/MiSeq-SOP-demo/actions/workflows/build.yml/badge.svg)](https://github.com/SchlossLab/MiSeq-SOP-demo/actions/workflows/build.yml)
[![license](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/SchlossLab/MiSeq-SOP-demo/blob/main/LICENSE.md)
<!-- badges: end -->


## Dependencies

- mothur
- R
- snakemake

R packages:

- here
- schtools
- tidyverse


## Re-using this template

If you re-use this template for a real project, you'll need to fill in some
information in the following files:

- [LICENSE.md](LICENSE.md)
    - `YEAR`
    - `AUTHORS`
    - `FIRST_AUTHOR_LASTNAME`
    - `GITHUB_URL`
- mothur-snakemake-workflow.Rproj - rename this file to match your project.
- [paper/head.tex](paper/head.tex)
    - `RUNNING TITLE`
    - `FIRST AUTHOR LASTNAME`
    - `AUTHORS AND AFFILIATIONS`
- [paper/paper.Rmd](paper/paper.Rmd)
    - `TITLE`
    - Write the actual text of your paper. 🤓
- [paper/references.bib](paper/references.bib) - export your references from Zotero (or other reference manager) to this bibtex file.
- README.md - don't edit this by hand, it's created by knitting [README.Rmd](README.Rmd).
- [README.Rmd](README.Rmd).
    - `mothur-snakemake-workflow` - your project slug.
    - Change the text as you see fit to explain your project.

## Directory Structure

```{bash tree, echo = FALSE, comment = ""}
tree -L 2 -n
```


## Workflow


See [config/README.md](config/README.md) for instructions on configuring this workflow for your own dataset.


<!-- run workflow/scripts/plot_rulegraph_dag.sh to generate this -->

![rulegraph](figures/rulegraph_demo.png)