Specify output directory or base name for SAMBA

[W-L]

Hi! Thanks for your great work on the whole toolkit! This is very similar to #281, but for SAMBA. Currently, the output is placed in the current working directory and the output files are named by the input contig-file without a way to change either. This makes it a bit awkward to use in pipelines/workflow managers, especially when different query files are used on the same contigs. As a workaround, I currently duplicate and rename the input contig file for each query file that I use for scaffolding, which could be avoided by the possibility to redirect the output or specify some base name for the output files. Like in the other issue, not really urgent but would be nice to have.

Thanks!