Fix for ParallelCmds.join when a cmds has failed.

Prevent calling join() on an AtomicCmd that has not been started,
due to the failure of an earlier command in the sequence.
Make GATK depend on sequence dictionary file.

GATK Indel realigner nodes now depend on the presence of a .dict
file for the reference sequence. If this file does not exist,
GATK would attempt to create it, which would cause problems when
running multiple instances.
Adding support for picard BuildSequnceDict.
Add ref. seq. dict. creation to BAM pipeline.
Initial support for rescaling Qs with mapDamage.