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Export five-dollar-genome-analysis-pipeline to Workspace

When I try to export the Export five-dollar-genome-analysis-pipeline to my Workspace, I am getting the message:

You don't have access to any published configurations for this method.

The only option available is to use a blank configuration.

How do I get access to a published configuration for this pipeline?

Also, is each read group suppose to be in a separate ubam for a given sample. So if I have 3 RG for a sample, I need to upload 3 ubams to the workspace google bucket. The reads have the RG so it would seem unnecessary to split them up.

Or could you place multiple RG in a bam from the same sample so just one ubam is uploaded with all 3 RGs?

Answers

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin
    edited February 2018

    We do have a published configuration for this method, however it is located inside a workspace that we are currently working on making public. As mentioned on this thread making a workspace public currently requires a system admin. I will come back and let you know as soon as we are able to make the five-dollar-genome-analysis-pipeline workspace public.

    With regards to your questions about read groups, I will have to ask someone who developed the method. I will get back to you soon on that as well.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin
    edited February 2018

    My colleague has just made the method configuration public--while we wait for the workspace itself to be made public here shortly, you should have access to the configuration.

    Edit: Workspace is now public. You should be able to find it under the Featured Workspaces tab.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    I've reached out to one of the people who helped to write that pipeline, and he said that you can have all your RGs in one ubam. It won't be scientifically invalid, but it may end up making the pipeline cost a bit more. The workflow is most efficient when your ubams are split by readgroups.

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