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
- Read through
modules/ww-rmats-turbo/ww-rmats-turbo.wdl to understand what rmats_post does and what inputs it expects
- Look at the existing
modules/ww-rmats-turbo/testrun.wdl to see how the other tasks are wired together
- Add a
call to rmats_post in testrun.wdl, connecting it to the outputs of the existing tasks where appropriate
- 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
Description
The
ww-rmats-turbomodule currently tests 3 out of 4 tasks in itstestrun.wdl(rmats,rmats_prep, andrmats_stat), but thermats_postpost-processing task is not covered.What needs to happen
modules/ww-rmats-turbo/ww-rmats-turbo.wdlto understand whatrmats_postdoes and what inputs it expectsmodules/ww-rmats-turbo/testrun.wdlto see how the other tasks are wired togethercalltormats_postintestrun.wdl, connecting it to the outputs of the existing tasks where appropriatemake run_sprocket NAME=ww-rmats-turboHelpful context
rmats_postis a post-processing step, so it likely consumes outputs fromrmats_prepand/orrmats_statww-splicing-proteomicspipeline inpipelines/also uses rMATS tasks and may provide additional contextSkills you'll practice