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Next Steps

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Congratulations on completing the Troubleshooting Workflows mini-course.

1. Apply the toolkit to your own pipelines

The fastest way to internalise these techniques is to reach for them on your own work. Next time a pipeline of yours fails, before reaching for the search engine:

  • Read the error message all the way through, then find the work directory it cites.
  • Walk through .command.sh, .command.err, .command.out, .exitcode, and ls before changing any code.
  • If the error is opaque or absent, run with -preview and then debug true to confirm what your code actually sees.

You'll find that the toolkit answers most questions on its own.

2. Build debugging into your workflow design

A few habits make pipelines easier to debug from the start:

  • Ship every process with a stub: directive so -stub-run always works.
  • Add a debug profile to your nextflow.config (real-time output, cleanup = false, maxForks = 1) so a single flag gets you full visibility.
  • Use .view() liberally during development. Remove it once channels are stable.

3. Continue your Nextflow training

If you haven't already, check out our other training material:

Additional resources