Debug nextflow in intellij

[Elisabeth Ortega]

Dear all,

I'm trying to play a little bit with the nextflow code to customize some stuff but I cannot manage to setup the debugger in intellij.

That's my config:

But after executing this it says:

Task '.launch.sh' not found in root project 'nextflow-prj'.

(I'd tested with and without a dot before launch.sh).

For sure I'm missing something in the configuration or I'm pointing to the wrong file.

Can anyone give me 5 cents on that?

Thanks,

Elisabeth

-----------------------------------------------------------

Elisabeth Ortega Carrasco • Computational Scientist

elisabet...@hpcnow.com 

www.hpcnow.com

--------------------------------------------------------------

[Paolo Di Tommaso]

Interactive debugging is not currently supported for Nextflow scripts 

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[Elisabeth Ortega]

Sorry, I didn't explained well myself. I'm not trying to debug a nextflow script, I'll debug nextflow code.
I'm building a new executor created by myself with new taskconfig properties and I'm getting a javaNullPointerExeception that I don't understand. This is why I want to use the debug, to try to find the origin and do a better follow up of variables rather than printing them in the log.

El dia dimecres, 26 de gener de 2022 a les 9:50:30 UTC+1, paolo.d...@gmail.com va escriure:

[Paolo Di Tommaso]

I see, than it easy, after compiling the code run 

````

./launch.sh -remote-debug run some-script.nf 

```

And connect with intellij remote debugger on port 8010 

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[Elisabeth Ortega]

Fantastic! now I can debug!

Thank you so much, Paolo!

Missatge de Paolo Di Tommaso <paolo.d...@gmail.com> del dia dc., 26 de gen. 2022 a les 11:25:

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[Paolo Di Tommaso]

Nice to read that. Consider using the discussion forum on the GitHub project for further questions.

Happy nextflow hacking! 

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