Finalize workflow for metaproteomics v2

ssarrafan commented 3 years ago

Finalize WDL

ssarrafan commented 3 years ago

This issues is related and the final part of issue #5 from the May sprint.

ssarrafan commented 3 years ago

@anubhav0fnu and @pdpiehowski I don't see any updates on this issue so I'm adding the backlog label so it can be reprioritized. Let me know if it's done and shovel be closed.

anubhav0fnu commented 3 years ago

@anubhav0fnu and @pdpiehowski I don't see any updates on this issue so I'm adding the backlog label so it can be reprioritized. Let me know if it's done and shovel be closed.

@ssarrafan, I updated the codebase, added the

report(peptide, protein, qc_metric) generation code to it
restructured the workflow

Things, I'm currently working on and would like to move to the next sprint

I'm testing the improvements with a few dry runs on our dataset(stegen). Workflow components work individually fine but running them together is something I'm currently working on especially after adding the report generation code.
regarding writing a Cromwell-WDL, I'm still figuring out a way to execute commands for multiple containers.
Working on metaproteomics-v2 README.
adding test data.( large(still a topic of discussion) & small(uploaded to NMDC google drive))

anubhav0fnu commented 3 years ago

@ssarrafan @pdpiehowski , I rolled out the v2.

microbiomedata / metaPro

Finalize workflow for metaproteomics v2 #6