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Nextflow Language Server Compliance for Freec Modules #9017

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Merged
merged 8 commits into from
Sep 8, 2025
Merged

Nextflow Language Server Compliance for Freec Modules #9017

merged 8 commits into from
Sep 8, 2025

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@FriederikeHanssen
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@FriederikeHanssen FriederikeHanssen commented Sep 8, 2025

New take on #8917

PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review September 8, 2025 15:29
@maxulysse maxulysse added this pull request to the merge queue Sep 8, 2025
Merged via the queue into master with commit b9cec8b Sep 8, 2025
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@maxulysse maxulysse deleted the freec_the_second branch September 8, 2025 15:45
@maxulysse maxulysse mentioned this pull request Sep 9, 2025
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chaochaowong pushed a commit to chaochaowong/modules that referenced this pull request Sep 30, 2025
@FriederikeHanssen @chaochaowong
Nextflow Language Server Compliance for Freec Modules (nf-core#9017)
c6bfc26 
* format test config

* lint assesssignificance

* lint freec2* and makegraph*

* lint freec

* see if we can find a middle ground between language server and what works

* try the old way

* add null check back

* use getAt explicitely
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@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @maxulysse