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Back-merge the 4.0.3 security patch into dev - #98

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mashehu wants to merge 6 commits into
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backmerge-security-patch-4.0.3
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Back-merge the 4.0.3 security patch into dev#98
mashehu wants to merge 6 commits into
devfrom
backmerge-security-patch-4.0.3

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@mashehu

@mashehu mashehu commented Jul 28, 2026

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Forward-ports the merged master security patch into dev so the fix is a shared ancestor and the coming removal of the momentarily ignored lint tests (coming with nf-core/tools 4.1.0) propagates cleanly.

jannikseidelQBiC and others added 6 commits November 8, 2024 16:20
@jannikseidelQBiC
Merge pull request #45 from nf-core/dev
69f308c 
Release - 1.1.0
@d4straub
Merge pull request #76 from nf-core/dev
698eedc 
Release 1.2.0
@d4straub
Merge pull request #88 from nf-core/dev
3586921 
Release 1.3.0
@nf-core-bot
Remove vulnerable PR-comment artifact pattern
5adff76 
These files conflicted with the patch and were reset wholesale to the nf-core/tools 4.0.3 template version, on the basis that they carry no pipeline-specific content. If this branch had local edits in them, those edits are gone — please review: .github/workflows/branch.yml .github/workflows/template-version-comment.yml
@mashehu
Merge pull request #97 from nf-core/patch
6fe2c11 
Remove vulnerable PR-comment artifact pattern
@nf-core-bot
Back-merge the 4.0.3 security patch into dev
95c9176
@mashehu
mashehu requested a review from d4straub as a code owner July 28, 2026 14:40
@github-actions

github-actions Bot commented Jul 28, 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: 3.4.1.
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 28, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 95c9176

+| ✅ 236 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗  18 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • schema_lint - Schema 'description' should be 'A pipeline to identify and remove certain sequences from raw genomic data. Default taxon to identify and remove is Homo sapiens.'
    Found: 'A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.'
  • schema_description - No description provided in schema for parameter: saveReference
  • local_component_structure - prepare_fasta4blastn.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - map_kraken2seqids_to_fqheaders.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - summary_classification.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - rename_fastq_headers_pre.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - merge_ids.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - kraken2preparation.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - isolate_kraken2_ids.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - filter_blastn_identcov.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - rename_fastq_headers_after.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - filter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - summarizer.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - summary_blastn.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - parse_kraken2report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - isolate_bbduk_ids.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2026-07-28 14:41:58

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@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

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@mashehu @jannikseidelQBiC @d4straub @nf-core-bot