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Important! Template update for nf-core/tools v3.5.1 #667

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Merged
sofstam merged 7 commits into from
Nov 21, 2025
Merged

Important! Template update for nf-core/tools v3.5.1 #667

sofstam merged 7 commits into from
Nov 21, 2025

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@nf-core-bot nf-core-bot commented Nov 20, 2025

Version 3.5.1 of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: https://nf-co.re/blog/2025/tools-3_5_0

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.5.1 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 v3.5.1 release page.

Note

Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository. Older template PRs will be automatically closed once a newer template PR has been merged.

jfy133
jfy133 reviewed Nov 20, 2025
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github-actions bot commented Nov 20, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7ef8b3e

+| ✅ 286 tests passed       |+
#| ❔   1 tests had warnings |#
!| ❗  19 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - Config manifest.version should end in dev: 1.2.5
  • 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 fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-11-20 14:41:57

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jfy133 commented Nov 20, 2025

@nf-core-bot fix linting

jfy133
jfy133 reviewed Nov 20, 2025
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CHANGELOG.md
Comment on lines 22 to +24
| Tool | Previous version | New version |
| ------- | ---------------- | ----------- |
| nf-core | 3.3.2 | 3.4.1 |
| nf-core | 3.3.2 | 3.5.1 |
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Suggested change
| Tool | Previous version | New version |
| ------- | ---------------- | ----------- |
| nf-core | 3.3.2 | 3.4.1 |
| nf-core | 3.3.2 | 3.5.1 |
| Tool | Previous version | New version |
| -------- | ---------------- | ----------- |
| nf-core | 3.3.2 | 3.5.1 |
| multiqc | 1.27 | 1.32 |

jfy133
jfy133 reviewed Nov 20, 2025
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jfy133 commented Nov 20, 2025

@nf-core-bot fix linting

@sofstam sofstam merged commit 7ab70ba into dev Nov 21, 2025
9 checks passed
@sofstam sofstam deleted the nf-core-template-merge-3.5.1 branch November 21, 2025 08:48
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@jfy133 jfy133 jfy133 left review comments

@dialvarezs dialvarezs dialvarezs approved these changes

@sofstam sofstam sofstam approved these changes

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

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