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docs: Command line arguments for configuration files #1343

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merged 3 commits into from Jan 28, 2022
Merged

docs: Command line arguments for configuration files #1343

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Command line arguments for configuration files
enryH Jan 20, 2022
b10eaa8
fix arg name
johanneskoester Jan 26, 2022
f3aa1da
fmt
johanneskoester Jan 26, 2022
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2 changes: 1 addition & 1 deletion docs/snakefiles/configuration.rst
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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 ``--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:
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