Copy metaAssembly wdl file to this repo and replace the assembler spades with megahit for metaT. about metat_assembly

[aclum]

What are the blockers from importing a wdl from JGI's repo instead of copy?

[mshakya]

sorry, didnt see this earlier. Is there an example wdl that imports directly from JGI (annotation one maybe?) ? Assembly and ReadsQC are nmdc specific that emulates JGI wdl. One method might be just git clone the wdls or just have dockers for wdls.

[mshakya]

Also, i have focused on using spades now.

[aclum]

none of the nmdc workflows do this now, we'd have to update the workflows to wdl version 1.0, this is straightforward, to be able to use url imports. I dont think we can have dockers for the wdls b/c you cant run docker within docker.

[mshakya]

I tried direct import like this:

import "https://raw.githubusercontent.com/microsoft/five-dollar-genome-analysis-pipeline-azure/az1.1.0/structs/GermlineStructs.wdl" as http_rnaspades

based on cromwell's HELPDOC, but was not able to get it working as the wdl file was not being accessed and obtained. I tried this with version 1.0 and same error.

I used git submodule instead, which i think also provides a cleaner alternative to copying.

Closing this issue for now.