mothur-snakemake-workflow

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

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
  • YEAR
  • AUTHORS
  • FIRST_AUTHOR_LASTNAME
  • GITHUB_URL
• mothur-snakemake-workflow.Rproj - rename this file to match your project.
• paper/head.tex
  • RUNNING TITLE
  • FIRST AUTHOR LASTNAME
  • AUTHORS AND AFFILIATIONS
• paper/paper.Rmd
  • TITLE
  • Write the actual text of your paper. 🤓
• 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.
  • mothur-snakemake-workflow - your project slug.
  • Change the text as you see fit to explain your project.

Directory Structure

.
├── LICENSE.md
├── README.Rmd
├── README.md
├── config
│   ├── README.md
│   ├── crc
│   ├── demo.yaml
│   └── slurm
├── data
│   ├── README.md
│   └── mothur
├── figures
│   ├── dag_crc.png
│   ├── dag_demo.png
│   ├── mothur-snakemake-workflow.png
│   ├── rulegraph_crc.png
│   ├── rulegraph_demo.png
│   └── stability_alpha-diversity.pdf
├── log
│   ├── hpc
│   └── mothur
├── mothur-snakemake-workflow.Rproj
├── paper
│   ├── head.tex
│   ├── mbio.csl
│   ├── paper.Rmd
│   ├── paper.md
│   ├── paper.pdf
│   ├── preamble.tex
│   └── references.bib
└── workflow
    ├── Snakefile
    ├── envs
    ├── notebooks
    └── scripts

14 directories, 21 files

Workflow

See config/README.md for instructions on configuring this workflow for your own dataset.