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Important! Template update for nf-core/tools v3.4.1 #657

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Merged
jfy133 merged 9 commits into from
Nov 4, 2025
Merged

Important! Template update for nf-core/tools v3.4.1 #657

jfy133 merged 9 commits into from
Nov 4, 2025

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@nf-core-bot nf-core-bot commented Oct 16, 2025 •
edited by jfy133
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Version 3.4.1 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.4.1 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.4.1 release page.

Will also close #659

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github-actions bot commented Nov 3, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 219d1e0

+| ✅ 287 tests passed       |+
!| ❗  18 tests had warnings |!
Details

❗ 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 - visualization_krona.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 - longread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/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_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
  • local_component_structure - standardisation_profiles.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_adapterremoval.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 - nonpareil.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

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-11-04 09:42:16

jfy133
jfy133 approved these changes Nov 4, 2025
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jfy133
jfy133 reviewed Nov 4, 2025
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@jfy133 jfy133 mentioned this pull request Nov 4, 2025
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@jfy133 jfy133 linked an issue Nov 4, 2025 that may be closed by this pull request
--version requires samplesheet and database samplesheet #659
Closed
@sofstam
Remove value of processes from default test snapshot
219d1e0 
Removed the numeric value 186 from the test snapshot.
@jfy133 jfy133 merged commit 52c8014 into dev Nov 4, 2025
7 checks passed
@jfy133 jfy133 deleted the nf-core-template-merge-3.4.1 branch November 4, 2025 10:39
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@jfy133 jfy133 jfy133 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

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--version requires samplesheet and database samplesheet

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