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chore: back-merge master security patch into dev - #1896

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pinin4fjords merged 6 commits into
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backmerge-security-patch-4.0.3
Jul 24, 2026
Merged

chore: back-merge master security patch into dev#1896
pinin4fjords merged 6 commits into
devfrom
backmerge-security-patch-4.0.3

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@mashehu

@mashehu mashehu commented Jul 24, 2026

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Forward-ports the merged master security patch into dev so the fix is a shared ancestor and the 4.1.0 lint-shim removal propagates cleanly.

pinin4fjords and others added 6 commits April 9, 2026 17:50
@pinin4fjords
Merge pull request #1765 from nf-core/dev
47b3b0d 
Dev -> master for nf-core/rnaseq 3.24.0
@pinin4fjords
Merge pull request #1816 from nf-core/dev
891468c 
Dev -> master for nf-core/rnaseq 3.25.0
@pinin4fjords
Merge pull request #1838 from nf-core/dev
e7ca462 
Dev -> master for nf-core/rnaseq 3.26.0
@nf-core-bot
Remove vulnerable PR-comment artifact pattern
15ade03
@mashehu
Merge pull request #1895 from nf-core/patch
1f03b53 
Remove vulnerable PR-comment artifact pattern
@nf-core-bot
Merge remote-tracking branch 'origin/master' into backmerge-security-…
f0c8d88 
…patch-4.0.3
@github-actions

github-actions Bot commented Jul 24, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Jul 24, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f0c8d88

+| ✅ 211 tests passed       |+
#| ❔  23 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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_todos - TODO string in base.config: Check the defaults for all processes
  • 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

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: conf/containers_conda_lock_files_amd64.config
  • files_exist - File is ignored: conf/containers_conda_lock_files_arm64.config
  • files_exist - File is ignored: conf/containers_docker_amd64.config
  • files_exist - File is ignored: conf/containers_docker_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_https_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_https_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_arm64.config
  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • nf_test_content - nf_test_content
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File does not exist: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-rnaseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-rnaseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_nf_test - actions_nf_test
  • modules_config - modules_config
  • container_configs - container_configs

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-07-24 13:16:33

pinin4fjords
pinin4fjords approved these changes Jul 24, 2026
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@pinin4fjords pinin4fjords left a comment

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Mechanical back-merge of the nf-core/tools 4.0.3 security patch (already merged to master in #1895) into dev. CI is green, diff matches the master fix. LGTM.

@pinin4fjords
pinin4fjords merged commit 3897963 into dev Jul 24, 2026
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3 participants

@mashehu @pinin4fjords @nf-core-bot