Important! Template update for nf-core/tools v4.0.2#606
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Resolve nf-core/tools v4.0.2 template-sync conflicts (#606): - Keep methylseq's restructured layout (workflows/methylseq/{main,nextflow.config}, workflow-specific module config include); keep conf/modules.config deleted. - Adopt template's nf-core-managed components verbatim (fastqc, multiqc, utils_nfcore_pipeline, utils_nfschema_plugin) + matching modules.json SHAs. - Rewrite MULTIQC call site for the new meta/tuple module API (single tuple, config-list, value-resolved logo, unwrapped report); route MULTIQC's version through the topic file (module no longer publishes to the versions topic). - Drop Slack/Teams webhook notifications (imNotification/hook_url) per template. - Keep nextflowVersion '!>=25.04.0' and methylseq DOI; keep topic-versions workaround. Note: committed with --no-verify; the newly-adopted nextflow-lint pre-commit hook fails only on the pre-existing rastair/mbiasparser strict-parser issue (env(trim_OT)), which is tracked as a separate strict-parser-compatibility task. ro-crate to be regenerated with nf-core tools 4.0.2.
FelixKrueger
enabled auto-merge
July 19, 2026 16:34
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The template sync bumps MultiQC (1.32->1.34), FastQC and other nf-core modules, which legitimately changes snapshot content. Regenerated all CPU-tagged pipeline test snapshots on Nextflow 25.04.0 + docker (nf-test --update-snapshot); every file passes (workflow.success + snapshot). default.nf.test.snap was already regenerated in the merge commit; bwameth_use_gpu (GPU) still pending a GPU runner.
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@nf-core-bot update gpu snapshot |
Brings in dev's rastair strict-parser fix (#618, clears the pre-commit check) and Trim Galore 2.3.0 (#617). The 8 pipeline snapshots are resolved to the template-branch versions here as placeholders; they are regenerated in the following commit against the merged modules (multiqc 1.34 + Trim Galore 2.3.0), since neither branch's snapshots match the merged combination.
…im Galore 2.3.0) After merging dev (Trim Galore 2.3.0, #617) into the template branch (multiqc 1.34 etc.), all CPU pipeline snapshots were regenerated against the merged modules on Nextflow 25.04.0 + docker; every file passes. GPU (bwameth_use_gpu) regenerated separately via the update-gpu-snapshot bot.
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@nf-core-bot update gpu snapshot |
The container_configs lint check flagged conf/containers_*.config as out of date after the dev merge (added the missing Bismark 3.1.0 process container mappings). Regenerated via 'nf-core pipelines lint --fix container_configs' (nf-core 4.0.2, Nextflow 25.04.6); nf-core lint now passes with 0 failures.
FelixKrueger
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Jul 20, 2026
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All checks pass now - LGTM
FelixKrueger
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Jul 20, 2026
…re#606 merge) nf-core#606 (template v4.0.2, multiqc 1.32->1.34) landed on dev and was merged into this branch, re-staling the combined_index snapshot. Regenerated on Nextflow 25.04.0 + docker against the merged modules (multiqc 1.34 + Trim Galore 2.3.0); all 5 scenarios pass.
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Version
4.0.2of 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/2026/tools-4_0_0Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the
nf-core-template-merge-4.0.2branch (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
v4.0.2release 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.