IKIM-Essen/RiboSnake

16S pipeline using qiime2 created with snakemake

Overview

Latest release: v0.11.0, Last update: 2026-07-12

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=IKIM-Essen/RiboSnake

Quality control: linting: passed formatting: failed

Wrappers: bio/fastqc bio/multiqc

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda package manager. It is recommended to install conda via Miniforge. Run

conda create -c conda-forge -c bioconda -c nodefaults --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

For other installation methods, refer to the Snakemake and Snakedeploy documentation.

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/IKIM-Essen/RiboSnake . --tag v0.11.0

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 3: Configure workflow

To configure the workflow, adapt config/config.yml to your needs following the instructions below.

Step 4: Run workflow

The deployment method is controlled using the --software-deployment-method (short --sdm) argument.

To run the workflow with automatic deployment of all required software via conda/mamba, use

snakemake --cores all --sdm conda

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.

For further options such as cluster and cloud execution, see the docs.

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.

General configuration settings

To configure the workflow to your needs, change the settings in config/config.yaml. The default parameters were determined by using test data holding a MOCK community as positive control. The parameters were set to values that allowed to retrieve all bacterial genera in the MOCK community.

Metadata sheets

You need to fill out the metadata.txt according to your needs. It holds all numeric and categorical metadata information of your data. Please be careful while filling out this file, and make sure you don’t miss a tab to separate the columns and look for spelling mistakes. Those can lead to problems in the analysis further down and are quite annoying to look for.

The two files sample_info.txt and sample.tsv, are filled out automatically, if the variable include-data-prep is set to true in the config file and you are running the command snakemake --cores $N --use-conda data_prep. Please set this variable to false when the data_prep step is done.

Linting and formatting

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