chore: template update to nf-core/tools 4.0.2#150
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Moved to docs/CONTRIBUTING.md
Update the nf-core template from 3.5.2 to 4.0.2 via a fresh `nf-core pipelines sync`. 4.0 changes applied: - nextflowVersion -> !>=25.10.4; add the wave profile - remove webhook notifications (hook_url, slackreport.json, adaptivecard.json, imNotification call); add workflow.onError handler - move CONTRIBUTING.md from .github/ to docs/ - switch git hooks to prek; ignore .lineage/ - regenerate nextflow_schema.json (custom params + descriptions preserved) - sync ro-crate-metadata.json description with the README Preserved fastquorum customizations: tuned process resources, igenomes CHM13, nf-fgbio plugin, samplesheet/UMI validation, fgbio modules, DOIs/contributors/docs. nf-core modules kept at current versions (fastqc/multiqc not bumped) to avoid the 4.0 MultiQC input-signature change; module updates are a separate follow-up. conf/containers_*.config removed: the 4.0 auto-generated container configs cannot be regenerated for this pipeline's modules (local fgbio modules lack meta.yml; kept nf-core modules predate the meta.yml containers block). Verified: nf-core pipelines lint (258 passed, 0 failed), prek hooks, nf-test --profile debug,test,docker (26/26 passed). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Updates the nf-core template from 3.5.2 → 4.0.2 via a fresh
nf-core pipelines sync. Supersedes the stale automated PR #149 (its merge branch predated recentdevwork).Notable 4.0 changes applied
nextflowVersion→!>=25.10.4; added thewaveprofilehook_url,assets/slackreport.json,assets/adaptivecard.json, and theimNotificationcall (the dormant helper remains in the kept nf-coreutils_nfcore_pipelineand is no longer used)workflow.onErrorhandlerCONTRIBUTING.mdmoved.github/→docs/prek;.lineage/added to.gitignorenextflow_schema.jsonregenerated (all custom params + descriptions preserved)Preserved fastquorum customizations
CHM13entry,nf-fgbiopluginlibrary_id/lane/flowcell, fgbio read-structure checks), non-random UMI support, fgbio modulesScope notes
nf-core modules updateis a sensible follow-up.conf/containers_*.configremoved: the 4.0 auto-generated container configs can't be regenerated for this pipeline's modules (local fgbio modules have nometa.yml; kept nf-core modules predate themeta.ymlcontainers:block). The pipeline uses per-modulecontainerdirectives as before; configs can be added when modules are updated. No lint rule was disabled.Verification
nf-core pipelines lint— 258 passed, 0 failed (14 warnings: newer-version-available + local-subworkflowmeta_yml, all pre-existing)prek run --all-files— prettier, whitespace, Nextflow Lint all passnf-test test --profile debug,test,docker— 26/26 passed, no snapshot changes🤖 Generated with Claude Code