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.

Will use the pegasus.change.dir profile option via `config.yaml`
instead.

This reverts commit c26ca54f.

The BLAHP submit wrapper creates a temp directory and cd's there
before running the executable. This breaks Pegasus jobs for a
sharedfs site as it expects to be in the shared-scratch dir
via the `remote_iwd` Condor ClassAd.  This dir is available via
the PEGASUS_SCRATCH_DIR env variable in the job, so cd there as a
workaround.

Condor jobs do not see normal user shell init scripts.  Have to
explicitly dot it in for module to work.

This reverts commit 1c068ff3.