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Command line arguments for configuration files
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- Is it `configfile` or `configfiles` ? 
- pattern `--config` of Markdown seems to be ``--config`` in RST (I will double check that with my previous commit)
- [API](https://snakemake.readthedocs.io/en/latest/api_reference/snakemake.html#api-reference-snakemake) references`configfiles`, but does not describe CLI parameter
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enryH committed Jan 20, 2022
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Expand Up @@ -39,7 +39,7 @@ In addition to the `configfile` statement, config values can be overwritten via
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
statement, or the ``--configfiles`` 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:
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@enryH enryH commented on f8f2627 Jan 20, 2022

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  • Is it configfile or configfiles ?
  • pattern --config of Markdown seems to be --config in RST (I will double check that with my previous commit)
  • API referencesconfigfiles, but does not describe CLI parameter

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