Important! Template update for nf-core/tools v4.0.2#156
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…-4.0.2 # Conflicts: # .github/workflows/awsfulltest.yml # .github/workflows/nf-test.yml # .gitignore # CHANGELOG.md # README.md # assets/multiqc_config.yml # conf/base.config # main.nf # modules.json # modules/nf-core/multiqc/environment.yml # modules/nf-core/multiqc/main.nf # modules/nf-core/multiqc/meta.yml # modules/nf-core/multiqc/tests/main.nf.test.snap # nextflow.config # ro-crate-metadata.json # subworkflows/local/utils_nfcore_riboseq_pipeline/main.nf # subworkflows/nf-core/utils_nfschema_plugin/main.nf # subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config # tests/nextflow.config # workflows/riboseq.nf
…neage [skip ci] These four .conda-lock files came in as non-conflicting additions from the nf-core-bot template-only branch during the merge. They correspond to a multiqc version this pipeline never installs (we kept dev's newer 1.35 pin), so nothing in the tree references them.
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pinin4fjords
approved these changes
Jul 6, 2026
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Version 4.0.2 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/2026/tools-4_0_0
Please 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.
Merge conflicts resolved
devhad diverged heavily since the last template sync (3.5.1), so most conflicts were between template infrastructure changes and the pipeline's own restructuring (workflow moved toworkflows/riboseq/main.nf, dozens of new local/nf-core modules for the ORF-catalogue and DTE work). Resolution followed the same rule throughout: adopt template infra improvements, keep pipeline-specific content, and where a template-tracked module/subworkflow had already been independently updated ondevpast what this template branch had (multiqc,utils_nfschema_plugin), keptdev's newer version.Adopted from template:
!>=25.10.4, GitHub Actions matrix andaction-tower-launchSHA pin updated to matchhook_url/imNotificationTeams/Slack webhook feature removed pipeline-wide (dropped fromnextflow.config,PIPELINE_COMPLETION,main.nf,awsfulltest.yml's Slack step already used the newer inline config)base.configretry exit-code range widened to175..177get_started/runningdocs restructure), README/ro-crate badgesKept from
dev:workflows/riboseq/main.nfrestructure (this PR'sworkflows/riboseq.nfwas deleted ondevas part of that work; the template's changes to it — mainly theMULTIQCsingle-map-input signature — were already present in the new file, done independently ahead of this sync)multiqc(1.35) andutils_nfschema_pluginmodule content/git_sha, both newer ondevthan in this template branchmaxRetries = 2inbase.config, real DOI/changelog/README content, pipeline-specifictests/nextflow.configCI test-data overrides, thegtf_hybridmerge_gffcompare/orftable_fasta_gtf_buildorfcatalogueincludeConfiglinesRegenerated after merge:
ro-crate-metadata.json,conf/containers_*.config(nf-core pipelines lint --fix container_configs). Also dropped 4 stale multiqc.conda-lockfiles that came in as non-conflicting additions from this template branch's now-discarded multiqc 1.34 pin.Known issue, not introduced by this merge: the
nextflow-lintpre-commit hook fails on the merge commit againstsubworkflows/nf-core/utils_nextflow_pipeline/main.nf(groovy.json.JsonGenerator.Options is not defined). That file is unmodified nf-core-template content;nextflow linton Nextflow 25.10.x can't resolve this nested Groovy class, fixed upstream only in 26.04.0+ (nextflow-io/nextflow#6744). nf-core/modules#11532 hit the identical failure on the same line and force-merged past it. Skipped just that one hook (SKIP=nextflow-lint) for the merge commit; every other pre-commit check ran normally.nf-core pipelines lintis clean (0 failures) after the container-config regeneration.