The wildcards in each rule should be COMPLETELY INDEPENDENT from user-defined filenames. Otherwise, setting the filenames is not really user-friendly, while these final output names are not important to our workflow. The wildcards in our scripts only determine dependencies between rules and the intermediate results.
In short, it should not be the filenames but the __variables (eg. software, tmp_d...etc)__ listed in the config file that play the roles in determining the rule wildcards.
thkuo
commented
6 years ago
The wildcards in each rule should be COMPLETELY INDEPENDENT from user-defined filenames. Otherwise, setting the filenames is not really user-friendly, while these final output names are not important to our workflow. The wildcards in our scripts only determine dependencies between rules and the intermediate results. In short, it should not be the filenames but the __variables (eg. software, tmp_d...etc)__ listed in the config file that play the roles in determining the rule wildcards.