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.

Bwa args

See merge request !1

Conflicts:
	chipathlon/workflow_job.py

Revert "Fixed minor spacing issues in workflow.  Added profiles for jobtime and memory into workflow_ob."

This reverts commit 85ee93ae.

This reverts commit 11f541a8.

This reverts commit 72808100.

With symlinking enabled, Pegasus will try to symlink the file
even though it's an http:// LFN, which doesn't work.  Add the file
with a different site name so Pegasus will download it properly.