12.6 Troubleshooting

unknown parameter in configfile runScript:
Make sure you have the runScript keyword and the mode spelled correctly in your config file. If you have opened/created the file e.g. on a windows file system, hidden file endings could be the reason. Run dos2unix config.yaml

Command ‘snakemake’ not found, but can be installed with:
Check if you activated the conda environment

AttributeError: ‘str’ object has no attribute ‘name’
You might have hit this recent bug described here: https://github.com/snakemake/snakemake/issues/1899
Try update tabulate e.g. with mamba install 'tabulate=0.8.10'

‘Workflow’ object has no attribute ‘use_env_modules’
You are using an old snakemake version. If you activated the provided conda environment and it still doesn’t work, re-load snakemake via mamba (from within the conda environment):
mamba install -c bioconda snakemake