seqeralabs

End-to-end workflow for fixing GitHub issues on the nf-metro repo with diagnostic rigor. Use when the user references a GitHub issue (by number, URL, or description) and wants it fixed. Handles worktree setup, a reused persistent env (no per-issue env creation), diagnostic-first investigation, authoring-mistake-vs-engine-bug triage (never dodge an engine bug by doctoring the reproducer), invariant-test-first implementation, runtime validators, evidence-cited fix verification, /simplify pass, full-repo lint, visual review via render preview, narrow-the-fix iteration on regressions, cost discipline (targeted tests, CI render-diff over local gallery rebuilds, skip-ci on WIP), scope discipline that fixes adjacent fallout in-session via delegated subagents instead of deferring it to a child issue, standalone issue-body hygiene, additive-only PR hygiene (no force-push, no narrative comments), clean execution of an authorised admin-merge (preserve history, no CI re-run), origin verification after every push, and PR

Diagnose and un-stick GitHub Pages publishing for nf-metro when a PR render preview or the docs site isn't updating. Use when a `_pr/<N>/` preview 404s or shows stale content, the "render preview is ready" link doesn't work, the docs site didn't refresh after a merge, or you suspect a Pages build stalled. Trigger on phrases like "the preview isn't updating", "the render preview link is broken", "check the pages ci", "poke the pages build", "docs site is stale", "did my preview publish". Covers the legacy-builder stall (the usual culprit), the re-trigger fix, the pr-renders -> pr-render-publish -> build chain, the render content marker, and the CDN caching gotchas that make verification misleading.

End-to-end release workflow for nf-metro. Checks the bioconda recipe for missing deps and bumps its build number if needed, bumps version in pyproject.toml and __init__.py, drafts a docs/releases/<version>.md page from the git log since the last tag (with illustrations where relevant), wires it into mkdocs.yml nav and the releases index table, then opens a PR. After merge, reminds you to create the GitHub Release. Trigger on phrases like "cut a release", "release X.Y.Z", "prepare release", "bump version to X.Y.Z".

Run a routing gate-arm triage slice on nf-metro - give every un-exercised branch arm in a layout/routing module a verdict (reachable -> author a fixture, defensive, candidate-dead, or reachable-but-defective -> file a bug). Use when the user wants to triage routing gate arms, close coverage-matrix gaps, work a

Wire an nf-metro diagram into an nf-core (or any Nextflow) pipeline repo - the mechanical pipeline-side setup, not the authoring of the .mmd itself. Use whenever the user wants to add nf-metro tooling to a pipeline (assets/metro_map.mmd, docs/dev/metro_map.md, the rendered SVG/PNG/animated assets, README image swap, CHANGELOG entry), replace an existing workflow.png/svg with a metro map, mirror the nf-core/rnaseq setup on a new pipeline, or pin nf-metro to a named branch of a fork while waiting for upstream fixes to land. Trigger on phrases like "set up nf-metro on pipeline X", "wire the metro map into the repo", "replace workflow.png with a metro map", "ship the metro diagram in pipeline Y", "pin nf-metro to my fork branch while we wait for the fixes", "what assets do I need in docs/images for the metro map".

Local visual regression check for layout or rendering changes. Renders all gallery examples, pixel-diffs against main, and opens changed renders as BEFORE/AFTER pairs. In most cases the CI render preview on a PR is sufficient - use this skill only for pre-push confidence on risky changes or when the user explicitly asks for a local diff.

Spin up the Astro / Starlight documentation site locally for live preview, optionally for a specific nf-metro branch. Use when the user wants to run, serve, preview, or develop the docs site (website/) - phrases like "serve the docs", "spin up the site", "run the docs locally", "preview the website", "start the astro server", "preview the docs for branch X / this PR", or when iterating on docs content, theme/layout overrides, or the gallery/pipelines/playground pages and wanting to see changes in a browser. Wraps scripts/serve_docs.sh, which generates the git-ignored dynamic content (gallery, pipelines, playground manifest) before starting the dev server, and with --branch checks the branch out into an isolated worktree and installs its nf_metro so the renders reflect that branch.

Build a self-contained HTML triage page for failing/xfailing layout-invariant tests in nf-metro (test_label_x_anchored_to_station_marker_on_horizontal_runs, test_visual_stack_station_xs_share_column, test_row_trunk_marker_cy_consistent, test_no_kink_at_section_boundary, test_symfan_pairs_share_y, test_lines_dont_cross_non_consumer_markers, test_topological_siblings_share_y_or_symmetric, test_section_bbox_has_bottom_padding, test_off_track_inputs_above_consumer). Each row pairs the rendered fixture SVG with a red-bbox overlay on the offending element, a plain-English "Supposed issue" + "What to check" explanation, and bug / not-a-bug / ambiguous triage buttons whose state is saved in localStorage and exported as JSON. Use when the user asks to "triage layout invariants", "review xfails", "review failing layout tests", "build the triage page", or generally wants to triage the layout-invariant test suite by eye.

Rewrite technical product documentation to strip AI slop and conform to the CTRT topic-type model (Concept, Task, Reference, Troubleshooting) plus Tutorial. Use whenever the user wants to deslop, tighten, edit, or rewrite technical docs — concept pages, task / how-to pages, reference material (API, CLI, config tables), troubleshooting pages, runbooks, tutorials, release notes, or product README sections. Trigger on phrases like "deslop", "make this doc less AI-sounding", "edit this docs page", "tighten my draft", or "rewrite this in CTRT", whether the user pastes prose or points at a file (.md, .mdx, .rst, .adoc, .txt, .docx). Scope is product/technical documentation only — do not use for marketing copy, blog posts, social posts, or general prose. Default behavior is to classify the input by topic type, then apply a heavy rewrite per the type-specific rules. Supports an optional passive mode (light-touch: word- and sentence-level fixes only, no restructuring — trigger on "passive", "light-touch", "words only"

Apply Seqera docs house structural conventions to a documentation page or selection — page introductions, prerequisites, troubleshooting placement, admonitions, and other structural elements. Use when the user asks to format, clean up, standardize, restructure, or fix the structure of a docs page, or when writing a new guide/tutorial that needs to follow house format. Each structural area has its own reference file under references/.

Generate OpenAPI overlay files for Seqera Platform API documentation. Use when working with API documentation updates, analyzing comparison overlays from Speakeasy, creating operations/parameters/schemas overlay files, or updating API documentation for new Platform versions. Triggers include requests to generate overlays, document new API endpoints, analyze API changes, or work with Seqera Platform OpenAPI specifications.

Format and style-check open source Nextflow and Wave changelogs to ensure consistency in voice, tense, attribution, linking, and component-based organization. Use when formatting a changelog in changelog/nextflow/ or changelog/wave/.

Format and style-check Seqera Platform changelogs (Cloud and Enterprise only) for consistency in voice, tense, component-based organization, and formatting conventions. Use when formatting a Platform changelog, checking changelog style for Cloud or Enterprise releases, or working with files in changelog/seqera-cloud/ or changelog/seqera-enterprise/. Does not apply to Wave, Nextflow, or Fusion changelogs — use changelog-os-formatter for those.

Turn feature sources (Jira epics, PRDs, design docs, GitHub PRs) into documentation updates for Seqera Platform docs. Use this skill whenever the user wants to: write docs for a new feature, update existing docs based on a Jira epic or ticket, draft doc changes from a PRD or design doc, review PRs and write matching documentation, do a gap analysis between current docs and shipped features, create a change summary or changelog for doc reviewers, or says anything like "I need to do doc updates for this feature" or "can you draft docs from these sources". Also use when the user provides a mix of Jira links, Google Doc links, GitHub PR links, or uploaded PDFs and wants documentation produced from them.

Triage the doc impact of a single Seqera release against three surfaces: environment variables (does the change add/rename/remove/alter a var listed in seqeralabs/docs under platform-enterprise_docs/enterprise/configuration?), visual assets (do UI screenshots, recorded videos, or brand marks in the docs go stale?), and internal doc links (are page renames, moves, removals, or anchor changes breaking cross-page links?). Always use when the user gives a PR URL, Jira key, or changelog entry and asks what it breaks in the docs, or says: "check impact of this release", "run an impact check", "does this PR break docs", "is this a rebrand", "what docs does this affect", "what needs updating after this change", or "impact assessment". Also trigger on descriptions of a UI refresh, rebrand, env var change, page rename, or page removal. Prefer this over docs-state-assessment (broad audit) and docs-feature (drafts new content) for single-release triage.

Bump hard-coded version numbers across the Seqera docs in the two places they recur: (1) enterprise point releases — six files in platform-enterprise_versioned_docs/version-XX.Y/ that pin Docker image tags and Kubernetes manifests to a released version, plus the cloud-side functionality matrix that mirrors the enterprise compatibility table, and (2) the Connect client used by Studios — Dockerfile ARG defaults, docker build commands, prerequisite "or later" lines, and container-image tag samples scattered across platform-cloud/, platform-enterprise_docs/, and the versioned snapshots. Use when the user says: "bump the connect version", "version bump for 25.3.5", "what files do I need to update for the enterprise release", "where is the connect client mentioned", "scan for version numbers", or invokes this skill directly.

Troubleshoot IGV Studio issues in Seqera Platform. Use when studios fail to start, show errors, data not discovered, or browser console shows 404s.

Launch IGV Studio instances on Seqera Platform. Use when deploying IGV Studio, starting genomics visualization studios, or mounting data links to studios.

Browse, download, upload, and manage cloud storage data through Seqera Platform data links. Use when working with S3/GCS/Azure storage, mounting data to studios, or transferring genomic files.

Build Docker/OCI containers using Seqera Wave cloud build service. Use when building containers, Docker images, or when user mentions Wave, cloud builds, or needs to build without local Docker.

Rebuild nf-aggregate benchmark outputs locally from fetched JSON or external run dumps. Use when iterating on normalize/aggregate/render logic, chart changes, or benchmarking HTML output without re-running the full pipeline.

Fetch Seqera Platform run data for nf-aggregate and compare scheduling, runtime, task status, and cost patterns across runs. Use when investigating benchmark candidates, refreshing `.seqera/context`, or validating run-level differences before building a report.

Prepare correct nf-aggregate input CSV files for API runs, external tarballs, external directories, or mixed-source benchmarks. Use when comparing live Seqera runs against exported logs or building reproducible benchmark fixtures.