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Common issues
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Using singularity
=================
If you forget the ``--use-singularity`` flag for Snakemake, you will find that
many rules break due to the required tools not being available on your system.

Snakemake errors about reserved keywords
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If you install Snakemake manually instead of using Conda and the provided
``environment.yml`` file, you might get errors about reserved keyword that are
used in the Snakefiles. Please use the Snakemake version specified in the
``environment.yml`` file.