Pip 1631 new conda builder

[leepc12]

Compatibility for dockstore (Terra and DNAnexus)

• Can define docker image in input JSON

Since all tasks have docker attribute in runtime, old caper(<2.0) will not work with Conda and Singularity.
It will ignore conda, singularity in runtime and try to run pipelines with docker even on HPCs.

Main changes in this PR:

• To pass docker/singularity/conda to each WDL task.
• Conda environment builder script.
• DX workflow builder script.
  • -defaults defines input JSON, -extras defines workflow opts JSON. Removed -extras since we no longer need it to define default docker image for all tasks.
• Documentation
• Some changes in resource parameters (increased resource factors for gc_bias, spr)

[ottojolanki]

LGTM