Adapt for Nextflow 25.10.2

[matrulda]

Description
This PR makes sure that the pipeline is written in strict mode, which was enforced from Nextflow 25.10.
In addition to that:

• References and instructions for running tests locally have been updated
• Pull request template has been updated to a simpler one

Risk analysis
Very small change and tests are passing, no risks identified.

Validation procedure
Run pipeline on Miarka via the sequencing report service.

[nkongenelly]

Looks good.
I am assuming that the strict mode is it the default for nextflow v 25.10 or does it have to be passed in the nextflow command e.g from the arteria-sequencing-service that creates the nextflow command?

[matrulda]

Thanks for the review! 🙏

Looks good. I am assuming that the strict mode is it the default for nextflow v 25.10 or does it have to be passed in the nextflow command e.g from the arteria-sequencing-service that creates the nextflow command?

Strict mode in this context means that the nextflow pipeline syntax need to follow a specific format. It is enforced. Like python2 allowing print $var, while python3 enforces print($var). So we need to make sure that all nextflow pipelines we run uses format. The easiest way to do this is to test them with nextflow 25.10.+. Did this answer your question or did I misunderstand?

[nkongenelly]

Thanks for the review! 🙏

Looks good. I am assuming that the strict mode is it the default for nextflow v 25.10 or does it have to be passed in the nextflow command e.g from the arteria-sequencing-service that creates the nextflow command?

Strict mode in this context means that the nextflow pipeline syntax need to follow a specific format. It is enforced. Like python2 allowing print $var, while python3 enforces print($var). So we need to make sure that all nextflow pipelines we run uses format. The easiest way to do this is to test them with nextflow 25.10.+. Did this answer your question or did I misunderstand?

Oh perfect! Yes this answers my question. Thank you.