Moved whitelist parameters as input files

[vsmalladi]

Description

White list was hardcoded as gs paths. Made them defaults and moved to inputs for workflow so that they will be able to be inputed for different paths for azure.

---

Checklist

If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP documentation team by tagging either @ekiernan or @kayleemathews in a comment on this PR.

• Did you add inputs, outputs, or tasks to a workflow?
• Did you modify, delete or move: file paths, file names, input names, output names, or task names?
• If you made a changelog update, did you update the pipeline version number?

[dsde-jenkins]

Can one of the admins verify this patch?

[dsde-jenkins]

Can one of the admins verify this patch?

[kevinpalis]

LGTM!

[jessicaway]

Hi @vsmalladi,

I believe you are trying to make the pipeline flexible to accept whitelist files from sources other than GCP, is that correct?

The pipeline should already allow this.

The reason the defaults are listed outside the inputs section is to have the pipeline automatically select the whitelist based on the chemistry. This behavior and defaults can be overridden by explicitly providing a whitelist as input to the pipeline. Here is the input that allows this: https://github.com/broadinstitute/warp/blob/develop/pipelines/skylab/optimus/Optimus.wdl#L38

Does that address the concern you are trying to address with this PR or is there a further issue?

[vsmalladi]

Hi @vsmalladi,

I believe you are trying to make the pipeline flexible to accept whitelist files from sources other than GCP, is that correct?

The pipeline should already allow this.

The reason the defaults are listed outside the inputs section is to have the pipeline automatically select the whitelist based on the chemistry. This behavior and defaults can be overridden by explicitly providing a whitelist as input to the pipeline. Here is the input that allows this: https://github.com/broadinstitute/warp/blob/develop/pipelines/skylab/optimus/Optimus.wdl#L38

Does that address the concern you are trying to address with this PR or is there a further issue?

@jessicaway I get that, but then this assumes that the person knows about the files before trying to run the pipeline. Moving it to Inputs allows the files to be known by the user and UI in terra to have a user put in Azure or other location for the reference data.

[jessicaway]

@vsmalladi, I'm not sure I understand the distinction since the whitelist is already a pipeline input and Terra does not populate the default values in the input view. Regardless, we want to make this more flexible to be run in Azure as well as GCP, so an update to the current implementation will be needed.

Would you have a few min for a quick call sometime next week? It would be helpful to understand the Azure constraints so we can update this.

[vsmalladi]

@jessicaway yes lets do a call next week will reach out on slack.