From ad8aaa4853a150211513baecc474956575d326eb Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Fri, 28 Jan 2022 17:38:15 +0100 Subject: [PATCH] docs: Command line arguments for configuration files (#1343) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Command line arguments for configuration files - 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 * fix arg name * fmt Co-authored-by: Johannes Köster --- docs/snakefiles/configuration.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) 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: