Manually removing a module with rm -rf and then trying to re-install won't do anything because the module info is still in modules.json so an INFO message is printed to screen suggesting that the module is up-to-date even though it has been deleted.

Maybe a better solution is to check whether the module is installed first and re-install at the commit in modules.json if it isn't. It may be a good idea to tidy up modules.json "before" installing any modules just to make sure that we have the same modules listed in the JSON and installed locally.

$ nf-core modules install

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.0.2.dev0



? Tool name: fastqc
INFO     'nf-core/modules/fastqc' is already up to date                                                                                                     install.py:108