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Add test coverage for rmats_post task #268

Description

@tefirman

Description

The ww-rmats-turbo module currently tests 3 out of 4 tasks in its testrun.wdl (rmats, rmats_prep, and rmats_stat), but the rmats_post post-processing task is not covered.

What needs to happen

  1. Read through modules/ww-rmats-turbo/ww-rmats-turbo.wdl to understand what rmats_post does and what inputs it expects
  2. Look at the existing modules/ww-rmats-turbo/testrun.wdl to see how the other tasks are wired together
  3. Add a call to rmats_post in testrun.wdl, connecting it to the outputs of the existing tasks where appropriate
  4. Verify the testrun passes with make run_sprocket NAME=ww-rmats-turbo

Helpful context

  • rmats_post is a post-processing step, so it likely consumes outputs from rmats_prep and/or rmats_stat
  • Look at how the existing calls chain together to understand the data flow
  • The ww-splicing-proteomics pipeline in pipelines/ also uses rMATS tasks and may provide additional context

Skills you'll practice

  • Reading and understanding WDL task definitions and their input/output contracts
  • Wiring task outputs to downstream task inputs in a workflow
  • Understanding RNA splicing analysis workflows

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    good first issueGood for newcomerstestingUpdate involving the test run and/or linting CI/CD of the repo

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