Make it really easy to debug a single job

[jtratner]

Often with dxWDL, I want to be able to easily debug some task, especially by ssh'ing on to box with everything there.

Potentially useful ways to accomplish this:

1. Be able to specify a different docker image via secret parameter with a default (e.g., -i_image=... -iregistry_login=... or something) - this would make it easy to iterate rapidly on a prebaked image by pushing various things to external registry.
2. Dump fully templated script to a standard location so it can be edited and rerun. Include a script to run docker with correct commands. Docker image should be fully loaded locally and not deleted afterwards. Respect --debug-on.
3. Make it easy to do a "dxWDL clone", where you get hopped on to box with cromwell + your docker image + data downloaded + input JSON for cromwell. dxWDL debug-job -j job-123

[jdidion]

(1) is possible by adding a docker_image input parameter to your task with a default value, e.g.

task foo {
  input {
    String docker_image = "myimage"
  }
  ...
  runtime {
    docker: docker_image
  }
}

(2) is also supported, at least in dxCompiler. The job script is in /home/dnanexus/meta/commandScript.