Improve writing

[LouisLeNezet]

Description of feature

To match nf-core standards some code refactoring will need to be done.
Some of the nf-core modules has been patched but their modification could be avoided by adding the command in the config file by adding the value to the meta map, such as :
--subsample ${meta.subsample_fraction}

[atrigila]

Could you add an example of this? Which nf-core module?