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PacificBiosciences / pb-human-wgs-workflow-wdl

BSD 3-Clause Clear License
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Reorganization from CMH #78

Open williamrowell opened 1 year ago

williamrowell commented 1 year ago

I'm creating a draft pull request to make it easier to view and comment on the changes introduced by @byoo and @cbi-star.

Tagging @vsmalladi and @ducatiMonster916 for review.

cbi-star commented 1 year ago

@vsmalladi I will change the relative path as you suggested. Thanks!

All the relative "import" pathes have been adjusted here: https://github.com/cbi-star/pb-human-wgs-workflow-wdl/commit/9e77ad72bdd9da34f88113bd64558c1915389669

vsmalladi commented 1 year ago

For overall reorganization I would add the following to simpify. @williamrowell @cbi-star

I would also add a dockestore template so that its published on dockstore and highlights the workflow wdls and tests for the user community.

byoo commented 1 year ago

@vsmalladi @williamrowell @cbi-star

It sounds good to reorganize into workflows, tasks, and tests. How about reorganizing into workflows and tasks in this request and addressing remaining tasks in the follow-up pull requests? Creating tests doesn't look straightforward to me. We can save intermediate outputs from the test run using the data Billy prepared for us. But I don't have access to a publicly accessible storage for the tests and the Dockstore template. Also, the integration testing is taking long time to run. If possible, I'd like to have something closer to unit testing. Is there a way to execute a dry-run for a wdl workflow? If so, a quick test checking tasks' the command line and wdl syntax errors would be doable? Any comments would be appreciated!

vsmalladi commented 1 year ago

@byoo I think that would make sense. Do you want @cbi-star to do that in this PR or merge this and do a reogranization in another PR?

For the Dockstore template that is where @williamrowell would have to do.

byoo commented 1 year ago

@vsmalladi @williamrowell ,

@cbi-star and I would like to follow up with further reorganization later, primarily because testing takes couple days. Also, we would like to review PacBio's new initiative before making further efforts.

vsmalladi commented 1 year ago

@byoo should we have a meeting this week?

byoo commented 1 year ago

@vsmalladi, let's meet after reviewing the new pipeline. We will decide what to use in the (or near) future. Thanks a lot for your kind help!