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)
Compatibility for dockstore (Terra and DNAnexus)
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:
-defaultsdefines input JSON,-extrasdefines workflow opts JSON. Removed-extrassince we no longer need it to define default docker image for all tasks.gc_bias,spr)