Template for developing Snakemake workflows

Brief description of workflow

Required software environment

Standardized workflows are designed with minimal assumptions about the local software environment.

In essence, the following should suffice to get started:

1. Linux OS: Debian, Ubuntu, CentOS, Rocky and related distributions should be fine
2. Python3: modern is likely better; the current target version can be found in workflow/env/exec_env.yaml. Older versions may or may not work.
3. Conda: for automatic setup of all software dependencies
   • Note that you can run the workflow w/o Conda, but then all tools listed under workflow/envs/*.yaml [not dev_env.yaml] need to be in your $PATH.

For a detailed setup guide, please refer to the workflow documentation.

Internal (template) remark: adapt the above if the workflow deployment has additional requirements (e.g., Apptainer).

Required input data

Add info here - be concise, and provide more details in the workflow documentation.

Produced output data

Add info here - be concise, and provide more details in the workflow documentation.

Citation

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