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:

Hello Nextflow — Foundational Nextflow concepts
Hello nf-core — nf-core pipelines and best practices
nf-test — Add tests so future bugs are caught before they hit production
Other Side Quests — Deep dives into specific topics

Additional resources¶

Nextflow troubleshooting guide — official troubleshooting documentation
Nextflow channels reference — channel types and behaviour
Process directives reference — all available process configuration options
nf-test — testing framework for Nextflow pipelines
Nextflow Slack community — help from the community
Seqera Platform — monitoring and debugging at scale for production workflows