Add current physical/statistical phasing WDLs.

[samuelklee]

To support #1. Please include any version information and links in the PR, if possible.

[SHuang-Broad]

Does this work:
Link to the WDL residing in Hang's branch in this repo.
The phasing WDL imports other WDL files in that repo, so a literal copy might introduce fragmentation.

[samuelklee]

I think at this point a forked copy of the phasing-specific WDLs is warranted to speed development without having to worry about working in multiple repos. These WDLs are not currently being used in any other projects, correct? (In fact, I believe they are still living on a branch?)

If there are non-specific tasks, then perhaps just copying those tasks into this forked copy (perhaps accompanied by a comment) for now is fine. If those tasks are relatively stable, then when we move everything back to the original repo, it should be relatively easy to restore the dependencies. We might also want to rebase the branch or otherwise check that those dependencies are not already out of date (i.e., if they have been updated in the main branch).

[SHuang-Broad]

sounds reasonable.

I see in #9 @hangsuUNC did brought in all the WDL files used.
I think a better approach would be to consolidate all the needed tasks into a single WDL.

Thoughts? @samuelklee @hangsuUNC

[samuelklee]

Yes, I think moving all used tasks into a temporary task WDL that will only live in this repo should be fine. Alternatively, just place each task in its corresponding phasing-specific sub/WDLs as appropriate.

I’d recommend stripping out extraneous tasks like file finalization and keeping things minimal for now. I expect that we will want to do a round of refactoring (I think Hang and I discussed previoisly that some of the file-naming conventions could be changed to aid downstream analyses), followed by a round of dev work to start addressing the multiallelics.

[hangsuUNC]

sounds reasonable.

I see in #9 @hangsuUNC did brought in all the WDL files used. I think a better approach would be to consolidate all the needed tasks into a single WDL.

Thoughts? @samuelklee @hangsuUNC

sounds good to me.