diff --git a/docs/snakefiles/configuration.rst b/docs/snakefiles/configuration.rst index f609feed2..ec92a5c26 100644 --- a/docs/snakefiles/configuration.rst +++ b/docs/snakefiles/configuration.rst @@ -37,10 +37,10 @@ In addition to the `configfile` statement, config values can be overwritten via $ snakemake --config yourparam=1.5 Further, you can manually alter the config dictionary using any Python code **outside** of your rules. Changes made from within a rule won't be seen from other rules. -Finally, you can use the `--configfile` command line argument to overwrite values from the `configfile` statement. -Note that any values parsed into the `config` dictionary with any of above mechanisms are merged, i.e., all keys defined via a `configfile` -statement, or the `--configfile` and `--config` command line arguments will end up in the final `config` dictionary, but if two methods define the same key, command line -overwrites the `configfile` statement. +Finally, you can use the ``--configfile`` command line argument to overwrite values from the `configfile` statement. +Note that any values parsed into the ``config`` dictionary with any of above mechanisms are merged, i.e., all keys defined via a ``configfile`` +statement, or the ``--configfile`` and ``--config`` command line arguments will end up in the final `config` dictionary, but if two methods define the same key, command line +overwrites the ``configfile`` statement. For adding config placeholders into a shell command, Python string formatting syntax requires you to leave out the quotes around the key name, like so: