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Important! Template update for nf-core/tools v3.5.1#86

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Important! Template update for nf-core/tools v3.5.1#86
nf-core-bot wants to merge 7 commits intodevfrom
nf-core-template-merge-3.5.1

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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.

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nf-core-bot commented Mar 13, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Mar 13, 2026 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 94252d5

+| ✅ 201 tests passed       |+
#| ❔   4 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  17 tests had warnings |!
-| ❌   1 tests failed       |-
Details

❌ Test failures:

  • multiqc_config - assets/multiqc_config.yml does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/scnanoseq/releases/tag/1.0.0" target="_blank">nf-core/scnanoseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/scnanoseq/1.0.0/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="https://github.com/nf-core/scnanoseq/releases/tag/1.2.2" target="_blank">nf-core/scnanoseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/scnanoseq/1.2.2/docs/output" target="_blank">documentation</a>.

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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_if_empty_null - ifEmpty(null) found in /home/runner/work/scnanoseq/scnanoseq/workflows/scnanoseq.nf: _ ch_versions = ch_versions.mix (CAT_FASTQ.out.versions.first().ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/scnanoseq/scnanoseq/workflows/scnanoseq.nf: _ ch_versions = ch_versions.mix(FASTQC_NANOPLOT_PRE_TRIM.out.nanoplot_version.first().ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/scnanoseq/scnanoseq/workflows/scnanoseq.nf: _ ch_versions = ch_versions.mix(FASTQC_NANOPLOT_PRE_TRIM.out.toulligqc_version.first().ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/scnanoseq/scnanoseq/workflows/scnanoseq.nf: _ ch_versions = ch_versions.mix(FASTQC_NANOPLOT_PRE_TRIM.out.fastqc_version.first().ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/scnanoseq/scnanoseq/workflows/scnanoseq.nf: _ ch_versions = ch_versions.mix(FASTQC_NANOPLOT_POST_TRIM.out.nanoplot_version.first().ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/scnanoseq/scnanoseq/workflows/scnanoseq.nf: _ ch_versions = ch_versions.mix(FASTQC_NANOPLOT_POST_TRIM.out.toulligqc_version.first().ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/scnanoseq/scnanoseq/workflows/scnanoseq.nf: _ ch_versions = ch_versions.mix(FASTQC_NANOPLOT_POST_TRIM.out.fastqc_version.first().ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/scnanoseq/scnanoseq/workflows/scnanoseq.nf: _ ch_versions = ch_versions.mix(FASTQC_NANOPLOT_POST_EXTRACT.out.nanoplot_version.first().ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/scnanoseq/scnanoseq/workflows/scnanoseq.nf: _ ch_versions = ch_versions.mix(FASTQC_NANOPLOT_POST_EXTRACT.out.toulligqc_version.first().ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/scnanoseq/scnanoseq/workflows/scnanoseq.nf: _ ch_versions = ch_versions.mix(FASTQC_NANOPLOT_POST_EXTRACT.out.fastqc_version.first().ifEmpty(null))
    _
  • local_component_structure - align_longreads.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: docs/images/nf-core-scnanoseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-scnanoseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • template_strings - template_strings

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-13 19:54:02

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