snakemake-workflows/effect-size-estimation

Generic, uncertainty aware, parameter free effect size estimation

Overview

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Latest release: None, Last update: 2025-05-15

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Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install Miniforge. More details regarding Mamba can be found here.

When using Mamba, run

mamba create -c conda-forge -c bioconda --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

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/snakemake-workflows/effect-size-estimation . --tag None

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.

To configure the workflow, edit the config directory. It contains the config/config.yaml which has as central element the datasets section. In there, modify or add new subsections, each representing one dataset to process, with the intended dataset name as the key.

  • For each dataset define the path to a data table in .tsv format as can be seen in the example.

  • Define the columns that contain the variables to compare against using the variables key.

  • Define the column that contains the measurement data that shall be compared in terms of fold change and significance using the value key. The value key is optional and will be inferred automatically as the only non-variable column if left out.

  • Define the order in which variable values are compared and occur in the generated visualizations via the order key.

Outside of the datasets section you can set various technical parameters as instructed inside of the template config/config.yaml.

Linting and formatting

Linting results

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