Allow prefix in config file

[endrebak]

This allows users to run multiple analyses from the folder in which the Snakefile is located and the results from each will be put in different folder. They can also use the prefix to use another disk for storing the results with prefix='/mnt/different_folder'.

[wdecoster]

Good idea, but I wouldn't create a new index for each {prefix}... because that's a slow step which also takes quite some disk space. Can we keep those without {prefix}?

[endrebak]

If the files are different, you need to make different indexes, no? But I see your point.

If you want to avoid recomputation based on the names (by seeing that {sample}.index already exists) problems happen if people use the same names between analyses.

This is completely up to you :) I do not care either way. I can scrap the PR.

[endrebak]

We could think about this some more. No need to take a stance now :)

[wdecoster]

Sure, no rush for this one! If users reuse the sample name for different samples the that's on them ;-)

The current implementation also allows to analyze multiple regions by listing multiple regions in the config.yaml: