Adding in all the work from the long-term Special Project Malaria branch

[jonn-smith]

Merging in the long-running branch Kiran and I created for the malaria work.

I have attempted to put everything in reasonable places.

I know this is big, but I'm hoping to merge this fast so I can make a few updates to these pipelines on top of this branch.

[bshifaw]

1. Why are the set of pipelines in a folder called "Z_One_Off_Analyses" not integrated with the rest of the pipeline folder?
2. In some of the wdls I've commented to move the description to the meta block of the workflow, this is so the wdl doc page on the repository site is formated correctly. The automated documentation is sensitive to hashes at the top of the page.

[bshifaw]

Why are deprecated wdls being updated, are they used by any wdls in the main pipeline folder?

[jonn-smith]

I updated this so that miniwdl check would pass. I was running it on all wdls in the repo before I remembered that the deprecated folder was not being checked. It's not being used anywhere.

[SHuang-Broad]

I follow the same logic as Jonn.
That is, I validate locally too, including the deprecated ones. So if any of my changes makes the deprecated ones invalid, I'd do the minimal to make them valid but nothing more.
That being said, I don't fix bugs in those deprecated pipelines or tasks.

[jonn-smith]

@bshifaw The workflows and tasks in the Z_One_Off_Analyses folders are not supposed to be integrated into our main pipelines. They are for one-off analyses that I have needed to make for this work, but that we should not support. There is currently no better place to put them with them still being part of this repo (which they need to be).

[bshifaw]

remove the commented description lines at the top from wdl/pipelines/TechAgnostic/Utility/BenchmarkVCFs.wdl

[bshifaw]

👍