This document consolidates the expectations from the several files that are currently in the google drive.

Dashboard

• Title
• Overview Paragraph
• Experimental Design (required for analysis-focused workspaces)
• Data
  • Sample Data
  • Workspace Data
• Tools
• Tool Name Versions
• Notebooks
• Software versions
• Time and cost
• Contact Information
• Licensing

Example Dashboard

Template Document

WDL

• WDL is in a repository

  SCIENTIST IS PROVIDING THE REPO

  • Scientist has a method in the Firecloud Methods Repo

  • Scientist has uploaded wdl and json to Github

    • & made a workflow in Dockstore

  • Scientist has created a ReadMe for the repo

    Example README.md file for Scientist Repo

  COMMS TEAM IS PROVIDING THE REPO

  • Comms Team member has uploaded the wdl and json to terra-workflows github
    • & made a workflow in Dockstore.
  • Comms Team Member has created a ReadMe for the repo

• Repos containing WDL contain the Broad Licensing File or equivalent if covered under a different license.

Example Github Structure in terra-workflows

Example Workflow on Dockstore

Notebook

• All required dependencies are loaded
• Links to required startup scripts are provided
• The instructions for using environmental variables in the notebook are linked to inside the notebook.

Dataset

• Workspace Attributes Loaded into Workspace

  • References uploaded to a google bucket that are publicly accessible.
  • References correspond to input files (e.g. input bams are aligned to hg38, then reference should be hg38.)
  • Access to all attribute files should be public.

• Access to all dockers in the workspace attributes and WDLs should be public. Broadies Instructions

• Data Models loaded into Workspace

• Input and reference data uploaded to a google bucket.

  • Reference data sets required by the WDL and notebooks.
  • Test data sets to show that methods are working.
  • Directions on how to load full data sets into the data model provided in Dashboard
  • If data is not fully accessible to the public, the dashboard contains instructions on how to obtain credentials.

• Access to all test files and references should be public.

  • Public bucket owned and maintained by Scientist.
  • Public bucket owned and maintained by Comms Team

  Here is a code snipped that allows bucket owners to make their bucket public. The user needs to have Google SDK Tools installed on their local machine before running this code.

  gsutil acl ch -r -u AllUsers:R gs://path/to/bucket
  

Review - In addition to reviewing the checklist above

• All WDL Analysis run with the Datasets provided.
• All test datasets, Workspace attributes, reference data and dockers are publicly readable.
• If full data sets are not public, instructions on how to obtain access are in the dashboard.
• All Notebooks Run and generate plots with no additional ad hoc loading of packages
• The provided WDL/Inputs/Resources/Docker Images must be able to complete successfully with valid resultsFor example, variant callers should be calling variants in known locations for the input data.
• The summary of the pipeline and/or work provides enough detail for someone not knowledgeable about the method to be able to run it successfully.
• Relevant publications are linked in the dashboard.

Finishing Steps

• Have the Science Advisor look over the workspace and have them focus on making sure what’s written in the workspace summary is scientifically accurate and the generated outputs are correct.

• Have a person from Eds review workspace so that the workspace summary communicates its contents effectively

• Notify Eric Karofsky (erickarofsk@broadinstitute.org) (optional)

• Create a final version of the workspace by cloning the draft workspace created earlier in to the appropriate billing project ID (same as namespace).

  • Scientists Billing Project if hosted and maintained by their lab.
  • gatk-help if the workspace is hosted and maintained by Comms and related to GATK
  • OBJECT-NAME-TBD if the workspace is hosted and maintained by Comms and not GATK

• Get the final approval from Beri {for the moment, and possibly Tiffany, Robert, or Geraldine if there are higher level issues needing to be addressed}

• Make the workspace public (Beri, Tiffany, Sushma and Adelaide currently have permissions. One of these people need to be an owner on the workspace in order to make it public.

  Link to Swagger Location to Make Workspace Public

  

• Once it’s public, you can use the [Firecloud SOP on the dsde-docs wiki] (https://github.com/broadinstitute/dsde-docs/wiki/FireCloud-SOP) to make it featured.