add --target-file argument

[wikiselev]

Adding the --target-file argument requires an extra input to this module - a bed file. This commit adds the bed file input to the module.

[nvnieuwk]

Can you add some tests? Also will this bed input be the same for all files in the same channel?

[famosab]

I think this is very out of date and would close the issue. Feel free to open a new one if you want to change something on the samtools module :)