Move HCA pipelines to WDL 1.0

[kbergin]

This will cause ripple effects in the infrastructure because the adapters are not in WDL 1.0.

Move Optimus and SS2 to WDL 1.0

Why?

To have access to the latest features and for ease of maintenance going forward, and we need to update the pipeline to handle other assays in the future.

Where do I start?

• Main Optimus/SS2 WDL in skylab
• Optimus/SS2 WDL Tasks in skylab
• https://github.com/HumanCellAtlas/skylab/pull/310

ACs:

• All of Optimus is in WDL 1.0 including tasks
• All of SS2 is in WDL1.0 including tasks
• We create a new ticket to make adapters (this may go to Hornet)
• Confirm that tests run successfully

┆Issue is synchronized with this Jira User Story

[kbergin]

➤ Nick Barkas commented:

Based on discussions with Adam Nichols, this has the potential result in alot of downstream work as the adapters need to be updated as well and we need to ensure that we are not breaking Optimus in prod.

[kbergin]

An additional note here is that if we update to 1.0 we currently can’t put the workflow into Terra, but they are working to upgrade that.

[kbergin]

➤ Nick Barkas commented:

Most things, including ss2 single and multisample as well as Optimus work now. the SS2 tests for multisample, but not single sample fail and require further investigation

[kbergin]

Awesome!!!

[kbergin]

➤ Nick Barkas commented:

Optimus mouse tests fail because they are on older test script. Made ticket to fix separately.

[kbergin]

➤ Nick Barkas commented:

QA Instructions:

• checkout skylab
• run 1 optimus test run 1 ss2 test with ./test/trigger_test.sh

[kbergin]

➤ Jessica Way commented:

optimus PR test ( https://job-manager.caas-prod.broadinstitute.org/jobs/163f3644-1826-4c77-98c8-ca5addc5fc3a?q=id%3D163f3644-1826-4c77-98c8-ca5addc5fc3a ) and ss2 PR test ( https://job-manager.caas-prod.broadinstitute.org/jobs/2349811c-3f1d-4b43-90bf-8c405f49fa53?q=id%3D2349811c-3f1d-4b43-90bf-8c405f49fa53 ) both passed