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AnVIL CCDG WGS QC Freeze 2

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Jason Walker edited this page Oct 5, 2020 · 5 revisions

  • Claim a Workspace (please use Excel Online to make Edits): https://wustl.box.com/s/anx2yxg5goluu463sweftvhnlb6ij3vb

  • Find and clone the CCDG Workspace via anvil.terra.bio using a new name for the clone, ex. append _QC

  • Use the mgi-hall-ccdg-terra-qc2 billing project to ensure funding is correctly assigned to CCDG.

  • Navigate to Data, Add Reference Data, then add hg38 reference data to be included in the cloned workspace.

  • Navigate to Workflows, Find a Workflow, Find Additional Workflows, Dockstore: https://dockstore.org/workflows/github.com/genome/qc-analysis-pipeline:no_validatesamfile?tab=versions

  • Launch with AnVIL, select workspace name, confirm no_validatesamfile version,

  • Import example JSON file, see slack for AN example. NOTE: minor changes will be necessary for each workspace

  • Select root entity type, sample. Check box Delete Intermediate Files,

  • Update the following input entities on an as needed basis:

  • base_name (this should be the "sample"), ex. this.sample

  • input_bam (either a cram, cram_path or bam equivalent), ex. this.cram

  • SAVE

  • VALIDATE: Delete Intermediate Files is still selected

  • RUN ANALYSIS

  • Share the workspace with others. For this project use the MGI-CCDG-QC group. If additional folks need access to these workspaces, we should add them to this group.

  • Lather, rinse, repeat.

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