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Fix remaining linting warnings - #542

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nictru merged 4 commits into
devfrom
strict-syntax-warnings
Jun 1, 2026
Merged

Fix remaining linting warnings#542
nictru merged 4 commits into
devfrom
strict-syntax-warnings

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@nictru nictru commented May 12, 2026

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As strict syntax parsing is enabled by default since nextflow 26.04, strict syntax compliance has become more relevant. While #536 and #541 already made everything work correctly, there are still some warnings. This PR addresses them, while keeping the code functionally equal. The following changes have been made:

  1. Use lowercase channel instead of deprecated Channel for all channel constructors
  2. Remove usage of the implicit it iteration accessors in favor of explicit iterators
  3. Use underscore prefix for unused variables in operations such as .map()

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github-actions Bot commented May 12, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fbe6d72

+| ✅ 244 tests passed       |+
#| ❔   5 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 4.2.0
  • 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 CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • schema_description - No description provided in schema for parameter: skip_emptydrops

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-01 07:33:23

@nictru
nictru force-pushed the strict-syntax-warnings branch from 5f2fce5 to d38c554 Compare May 12, 2026 14:01
@nictru nictru mentioned this pull request May 12, 2026
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nictru requested review from fmalmeida and grst May 12, 2026 14:22
fmalmeida
fmalmeida reviewed May 12, 2026
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Comment thread subworkflows/local/align_cellrangermulti.nf
nictru added 3 commits May 12, 2026 19:58
@nictru
Merge branch 'dev' into strict-syntax-warnings
0909424
@nictru
Undo ch_gex_barcodes removal
2a92291
@nictru
Merge branch 'dev' into strict-syntax-warnings
fbe6d72 
Resolve conflicts in CHANGELOG.md (keep both chore entries) and
workflows/scrnaseq.nf (workflow fasta/gtf inputs with explicit closures).
@nictru
nictru requested a review from fmalmeida June 1, 2026 07:50
@nictru

nictru commented Jun 1, 2026

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I reverted the controversial channel removal so that we can get the main part of the changes merged, we can think about how to handle that later

fmalmeida
fmalmeida approved these changes Jun 1, 2026
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Thanks for the fixes.

@nictru
nictru merged commit e8070df into dev Jun 1, 2026
36 of 38 checks passed
@nictru
nictru deleted the strict-syntax-warnings branch June 1, 2026 09:39
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@fmalmeida fmalmeida fmalmeida approved these changes
@grst grst Awaiting requested review from grst

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