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Add strict syntax support#108

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nictru wants to merge 6 commits intodevfrom
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Add strict syntax support#108
nictru wants to merge 6 commits intodevfrom
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@nictru nictru commented Mar 31, 2026 •
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This is needed as nextflow 26.04 will enable strict syntax by default, leading to errors if requirements are not fulfilled. This PR makes the pipeline work in the new default settings. It also removes some strict syntax warnings.

Some information about what needs to be working can be found here

Only one category of strict syntax warnings remains: Unused variables in combination with the template structure. This is due to this issue

nictru added 6 commits March 30, 2026 10:39
@nictru
Fix nextflow lint errors
edf9b30
@nictru
Replace deprecated implicit closure parameter with explicit declarations
f24f465 
Nextflow now warns when using the implicit `it` parameter in closures.
Replace all occurrences with explicit named parameters (`val`, `name`)
in local subworkflows and the main workflow.
@nictru
Suppress lint warnings for intentionally unused closure and workflow …
afc0180 
…parameters

Prefix unused closure parameters and workflow take: inputs with `_` to
signal they are intentionally ignored, as required by the Nextflow linter.
@nictru
Remove dead channel variable assignments in hash demultiplexing subwo…
41f7198 
…rkflow

ch_assignments and ch_classifications were assigned by remapping HTODEMUX
outputs but never consumed. The raw outputs were already mixed directly
into ch_htodemux_assignments and ch_htodemux_classifications below.
@nictru
Update nf-core/subworkflows
bae2b12
@nictru
Fix nextflow help under strict syntax
173889f
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github-actions bot commented Mar 31, 2026

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 173889f

+| ✅ 359 tests passed       |+
#| ❔   1 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  16 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-03-31 06:33:25

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nictru commented Mar 31, 2026

I will need some help with getting the tests work @LuisHeinzlmeier

  1. Some files referenced in the tests (anymore)? To prevent such situations in future it would be helpful to include the commit hash in the test data references. You can look at scdownstream on how this is handled there
  2. The hashes seem to differe even if there are now 'functional' changes in this PR. Maybe the test assertions are overly strict? Or the test data was changed without updating the snapshots?

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