Commit 7d24d76f authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

continue README for tool descriptions

parent a7e1c446
......@@ -9,10 +9,13 @@ example file (usually containing default parameters that are set up on the `.rul
All Snakemake tool descriptions try to respect some rules and best practices in their design:
* First part correspond to all options that are set up from a `config.yaml` file
* First part correspond to all options that are set up from a `config.yaml` file. They all have the nomenclature `__TOOLNAME_variable`.
* Then the tool itself is described with:
* input with the nomenclature: `__TOOLNAME_input`
* output with the nomenclature: ` __TOOLNAME_output`
* params with different options that are described above
* There is usually a `exec_command` to give the possibility to change the way the tool is called (locally installed, singularity ...)
* There is usually a `options` to specify all other command line options
* the shell command
input and output are then set up in the Snakemake file that refer to the rule.
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