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sjspielman opened this issue Jun 2, 2025 · 0 comments · May be fixed by #1169
Open

Add script to create normal references for neuroblastoma #1147

sjspielman opened this issue Jun 2, 2025 · 0 comments · May be fixed by #1169
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If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.

Part of #1143

Describe the goals of the changes to the analysis module.

Following #1146, we will be ready to create normal references for SCPCP000004 to references/normal-references. This issue tracks adding a script to create the normal reference(s) identified in X.

Simultaneously, we'll need to add a project-specific workflow script to run SCPCP000004 samples through the module pipeline similar to what we have for SCPCP000015. We'll want to get the script that creates references running in this workflow script, which should also be added to run-analysis.sh.

By adding these scripts at the same time, we'll be able to have it tested in CI right away.

What will your pull request contain?

Two new scripts, one updated GHA, and associated documentation:

  • An R script in scripts to create and export normal references
  • A bash script in project-workflows to run this project, for now just with this step to create references
  • Updates to the module GHA to download the NB data needed for this code

Will you require additional software beyond what is already in the analysis module?

No

Will you require different computational resources beyond what the analysis module already uses?

No

If known, when do you expect to file the pull request?

Next 1-2 sprints

@sjspielman sjspielman self-assigned this Jun 2, 2025
@sjspielman sjspielman linked a pull request Jun 9, 2025 that will close this issue
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