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Coverage on nf-core#4520 pointed at three branches that cannot run. SequenceMatcher alternates equal and changed opcodes, so the block next to a change is always equal. The hold-back runs on a fresh workspace, so its snapshot is always empty and dropping the pending changes is enough. git only lists a changed file that one of the two commits has, so the "missing on both sides" case becomes an assert. Coding assisted with Claude Opus 5.5 Prompts (edited for grammar, private details removed): - 2026-10-15: "Fix the coverage reported on the PR."
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Covers the remaining branches Codecov reported on nf-core#4520: hunks that grow into or merge with a neighbouring change (inputs found by searching small texts, checked by applying the hunks), an empty template file, a template without .nf-core.yml, module files missing from modules.json, a pipeline without modules.json, the version line helpers, a branch with no template history, and the PR text for conflicting and partial migrations. The sync tests also pin that migrations run after the merge branch is created and before it is pushed. Coding assisted with Claude Opus 5.5 Prompts (edited for grammar, private details removed): - 2026-10-15: "Fix the coverage reported on the PR."
A template sync PR merges the new TEMPLATE commit into dev, and git's merge conflicts wherever the pipeline diverged from the template. These operations are the building blocks for applying a template update change by change instead: each inspects the pipeline first and reports applied, already applied, or conflict, so running it twice is safe and nothing is placed where it does not fit. nf-core modules and subworkflows are compared through modules.json and reported with the nf-core command to run, since pipelines often update them past the template's pinned version. Files nf-core generates become manual steps. Changes are held in memory until committed, so a conflict can be dropped without touching the pipeline. Ported from Skitionek/nf-migrate (32a6908, 2deb945), without that tool's per-pipeline placeholders: in sync, both template renders already carry the pipeline's own values. Coding assisted with Claude Opus 5.5 Prompts (edited for grammar, private details removed): - 2026-10-15: "Check out nf-core/tools, create a branch, port the commits from Skitionek/nf-migrate, and adapt them to run as part of the template update PRs that nf-core-bot opens."
The difference between two TEMPLATE commits is the template update. It is turned into operations that can be applied to a pipeline that has diverged from the template: each change keeps only as much context as it needs to be unique, and a replacement whose changed lines are unique keeps none, so an edit to a neighbouring line cannot block it. nf-core modules and subworkflows become component checks, since pipelines manage them with `nf-core modules`. The RO-Crate and container configs, which nf-core regenerates, and binary files become manual steps naming the command to run. The nf_core_version line is left out of the diff and stamped separately. Ported from Skitionek/nf-migrate (32a6908, 12804dc), generating operations directly rather than migration source files. Coding assisted with Claude Opus 5.5 Prompts (edited for grammar, private details removed): - 2026-10-15: "Check out nf-core/tools, create a branch, port the commits from Skitionek/nf-migrate, and adapt them to run as part of the template update PRs that nf-core-bot opens."
The template changes between the TEMPLATE commit a branch last merged and a new one are applied to that branch in a temporary worktree, and the result is recorded as a merge commit of the branch and the new TEMPLATE commit. Using the merge base rather than the previous TEMPLATE commit means a pipeline that skipped a sync still gets every change it lacks, as a git merge would. A conflict means no commit by default. With allow_conflicts the commit holds every change that fits; a file with any conflicting change is left as it was, because applying only some of a file's changes can leave it half converted. The report lists conflicts with the template change as a collapsed diff, and manual steps as a checklist. Ported from Skitionek/nf-migrate (b9f8773, 2deb945), applying one generated step instead of a chain of versioned migrations. Coding assisted with Claude Opus 5.5 Prompts (edited for grammar, private details removed): - 2026-10-15: "Check out nf-core/tools, create a branch, port the commits from Skitionek/nf-migrate, and adapt them to run as part of the template update PRs that nf-core-bot opens."
`nf-core pipelines sync --template-migrations` applies the template update to --from-branch change by change, after the merge branch is created from the new TEMPLATE commit. With `clean`, when every change applies, the merge branch moves to a merge commit of the pipeline branch and the template, so the PR opens without merge conflicts. With `partial`, it also moves when some changes conflict, keeping the changes that fit and leaving files with a conflicting change as they were. Otherwise the branch stays on the template commit, as before. The PR description gets a report of what happened, the conflicting changes with their template diff, and the remaining nf-core steps (module updates, RO-Crate and container configs) as a checklist. The option is off by default; the sync workflow passes `clean` for nf-core-bot PRs and lets a dispatch choose another mode. Replaces the GitHub Action of Skitionek/nf-migrate (b9f8773): the work happens while sync opens the PR instead of in a workflow reacting to it. Coding and writing assisted with Claude Opus 5.5 Prompts (edited for grammar, private details removed): - 2026-10-15: "Check out nf-core/tools, create a branch, port the commits from Skitionek/nf-migrate, and adapt them to run as part of the template update PRs that nf-core-bot opens."
Coverage on nf-core#4520 pointed at three branches that cannot run. SequenceMatcher alternates equal and changed opcodes, so the block next to a change is always equal. The hold-back runs on a fresh workspace, so its snapshot is always empty and dropping the pending changes is enough. git only lists a changed file that one of the two commits has, so the "missing on both sides" case becomes an assert. Coding assisted with Claude Opus 5.5 Prompts (edited for grammar, private details removed): - 2026-10-15: "Fix the coverage reported on the PR."
Covers the remaining branches Codecov reported on nf-core#4520: hunks that grow into or merge with a neighbouring change (inputs found by searching small texts, checked by applying the hunks), an empty template file, a template without .nf-core.yml, module files missing from modules.json, a pipeline without modules.json, the version line helpers, a branch with no template history, and the PR text for conflicting and partial migrations. The sync tests also pin that migrations run after the merge branch is created and before it is pushed. Coding assisted with Claude Opus 5.5 Prompts (edited for grammar, private details removed): - 2026-10-15: "Fix the coverage reported on the PR."
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PR checklist
CHANGELOG.mdis updated (PR number still to fill in)What
nf-core pipelines sync --template-migrations cleanapplies the template update todevchange by change, and when every change applies, the PR branch becomes a merge commit ofdevand the new TEMPLATE commit, so the template PR opens with no merge conflicts. The sync workflow passescleanfor nf-core-bot PRs; the option is off by default for local runs.The PR description gets a report either way: changes that conflict, each with its template diff, and the remaining
nf-coresteps (module and subworkflow updates, RO-Crate, container configs) as a checklist. When a change conflicts, the PR stays the plain template merge it is today.Why
git's merge conflicts wherever a pipeline diverged from the template, often only because a neighbouring line was edited. Here each template change is applied with the least context that keeps it unique, nf-core modules are compared through
modules.jsoninstead of patched, and files nf-core generates are left to its own commands.Decision
Migrations are generated during sync from the TEMPLATE commit
devlast merged to the new one, so each pipeline gets its own render (includingskip_features) and no migration has to be written per tools release. Apartialmode also pushes when some changes conflict, leaving those files untouched; the workflow usescleanbecause a pushed merge marks the template as merged, so changes left out would survive only in the PR description.Not in this PR
devmerged a template update and then reverted it (as nf-core/spatialaxe did with 4.0.2) still gets those conflicts, because git history says that template is merged.tests/pipelines/test_sync.pyalready fail ondevlocally: test pipelines start dirty because prettier fixes a double space in the template'sbranch.ymlafter the first commit. That needs its own fix; the new tests build their own git fixtures.Replaying nf-core/atacseq's 4.0.2 → 4.0.3 sync gives the merge its maintainers made, apart from their CHANGELOG entry and the RO-Crate, which the report lists as a manual step. The approach is ported from Skitionek/nf-migrate, whose validation replays 43 template merges from 11 pipelines.
Coding and writing assisted with Claude Opus 5.5