Sequenza tool: sequenza.R script is not exist

**Background**

In the “Sequenza detection” step, after `sequenza-utils.py` script invocation the `sequenza.R` script is called, which is also expected to be located in `sequenza` tool directory.

However, this script is not supplied with this tool. It looks like a custom script that should be located in a `/src/R` Fonda directory.

**Approach**

We suppose this script is also worth to add to `/src/R` Fonda directory for future third-party users.

Start with the Sequenza detection step and the invocation of sequenza-utils.py, then verify where sequenza.R is expected in the sequenza tool directory. Check whether the script should be added to the /src/R Fonda directory and confirm that the step can locate and invoke it for third-party users.

Written by the indexing model from the issue text.