Migrate example `Nextflow` workflow to DSL2

JustCommonUsername commented 4 months ago

Hi!

The test Nextflow scripts are outdated and cannot be run, as they use deprecated DSL 1. In order to keep workflows for local development runnable, I suggest migrating test workflows to DSL 2.

I will link this issue to PR with migration I did locally. It functioned well and workflows ran on locally deployed server, but you would probably like to do some housekeeping before merging😁

Version of Nextflow which throughs exception about deprecated DSL on my machine:

  N E X T F L O W
  version 24.04.1 build 5913
  created 20-05-2024 09:48 UTC (11:48 CEST)
  cite doi:10.1038/nbt.3820
  http://nextflow.io

JustCommonUsername commented 4 months ago

Unfortunately, it seems I don't have permissions to create branches and pull requests in your repo.

I am participant of StuPro_SS24_CalibraCurve project, in which we migrate the Calibra Curve workflow from KNIME to nf-cloud, so the change in local dev suite for workflows would be helpful for us.

Could you please look into it and provide me the PR permissions, so I could propose the change?

di-hardt commented 4 months ago

Please create a fork and create a PR from there. And thanks for the contribution 🙏

di-hardt commented 3 months ago

Accepted the PR! Many thanks

cubimedrub / macworp

Migrate example `Nextflow` workflow to DSL2 #13