diff --git a/tools/README.md b/tools/README.md index fe6c1a2fbfaee88bc33f2969943d6691eef4734c..8fce077b40204f4fb6689cd095d7b4d8622cf938 100644 --- a/tools/README.md +++ b/tools/README.md @@ -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. \ No newline at end of file