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Merged
merged 15 commits into from
Sep 12, 2025
Merged

Basic language server-syntax fixes #641

merged 15 commits into from
Sep 12, 2025

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jfy133
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@jfy133 jfy133 commented Aug 28, 2025 •
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This PR is the first one in a series to clean up our syntax to make it Nextflow language-server compliant.

It contains:

  • Using of workflow input channels rather than params (when exsiting)
  • Defining 'unique' variable names within operators rather than duplicating the same name as input channels
  • Using the 'unused variable' syntax for variables within operators (i.e. _FOO)
  • Ensuring local scope variables are defined correctly (and in a way the language server is satisfied)
  • Reduced a couple of places of essentially duplicated code

I envision three more follow up PRs:

  • Updating the currently syntax-problematic DIAMOND module
  • Fixing the input validation code and location of inputs to the main taxprofiler.nf workflow
  • Auto-formatting every file (once the previous PR is done)

PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/taxprofiler branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@jfy133
Revert "Move additional input validation to main workflow, and remove…
0e72e16 
… existance validation (as now done by nf-schema)"

This reverts commit 5bf0cd4.

:wq
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github-actions bot commented Aug 28, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 63dd897

+| ✅ 291 tests passed       |+
!| ❗  18 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • local_component_structure - kraken2_standard_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - krona_cleanup.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - longread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_filtering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_complexityfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - nonpareil.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - standardisation_profiles.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - visualization_krona.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-09-12 07:33:58

@jfy133 jfy133 requested a review from Midnighter August 28, 2025 10:43
@jfy133 jfy133 merged commit 9882905 into dev Sep 12, 2025
8 checks passed
@jfy133 jfy133 deleted the language-server-fixes branch September 12, 2025 08:23
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@maxulysse maxulysse maxulysse approved these changes

@sofstam sofstam Awaiting requested review from sofstam sofstam is a code owner

@LilyAnderssonLee LilyAnderssonLee Awaiting requested review from LilyAnderssonLee LilyAnderssonLee is a code owner

@Midnighter Midnighter Awaiting requested review from Midnighter

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