Fixed reference to undefined variable key in workflow_module.  Adjusted param files to use bed arguments

Fixed typo in remove_duplicates.yaml.  Adjusted get_full_name to handle no markers.  Updated workflow to track prefixes cross module.

Fixed workflow_module to work with single path modules.  Added new testing config files for paired_end reads.

Sai to sam args

`bwa samse` also requires the reference genome input files.

See merge request !2

The `bwa samse` command requires the reference genome inputs as well.