Commit 43145770 authored by Mei's avatar Mei
Browse files

explain 4 level config values

parent 3186e313
......@@ -117,6 +117,16 @@ It is also possible to set the `"species"` flag. Again, we will default to `unkn
# More advanced use of config files.
### 4 levels of configuring settings
In biopet, a value for a ConfigNamespace (e.g., "reference_fasta") for a tool or a pipeline can be defined in 4 different levels.
* Level-1: As a fixed value hardcoded in biopet source code.
* Level-2: As a user specified value in the config file (provided as an argument when running biopet command)
* Level-3: As a system specified value in the global config file ()
* Level-4: As a default value provided in biopet source code.
During execution, biopet framework will resolve the value for each ConfigNamespace following the order from level-1 to level-4. Hence, a value defined in the a higher level will overwrite the one define in a lower value.
### JSON validation
To check if the created JSON file is correct their are several possibilities: the simplest way is using [this](
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