Important! Template update for nf-core/tools v4.0.3 - #449
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This was referenced Jul 25, 2026
NicoDeVeaux
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Jul 26, 2026
Merge the nf-core/tools 4.0.3 template output (the same content as nf-core#449) so this branch lints clean against the current template rather than carrying files_unchanged exemptions for the pre-existing drift in .github/PULL_REQUEST_TEMPLATE.md and the two logo PNGs. Keeps the branch-local .nf-core.yml entries (bowtie2 snapshot merge_markers false positive, bamtools filter config defaults) and regenerates ro-crate-metadata.json. Drop this commit if nf-core#449 lands on dev first.
NicoDeVeaux
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Jul 26, 2026
Add entries for the Chromap read-group fix, the subread 2.0.1 pin and the deterministic consensus featureCounts column order. The template 4.0.3 bump is left to nf-core#449.
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Version
4.0.3of 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/advisories/pr-comment-workflow-vulnerabilityPlease make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the
nf-core-template-merge-4.0.3branch (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 the template sync documentation.
For more information about this release of nf-core/tools, please see the
v4.0.3release 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.