Honour process.resourceLabels in nf-seqera executor

[pditommaso]

Summary

Make the nf-seqera executor honour the standard Nextflow process.resourceLabels directive with cumulative semantics:

• The config-level process.resourceLabels baseline is attached once to the Sched run via CreateRunRequest.labels.
• Each task only sends the delta between its effective task.config.getResourceLabels() and the run baseline, on the new Task.labels field. Identical key/value entries are stripped; differing or new entries are sent so the scheduler's task-over-run merge gives the correct final values.
• Removes the now-redundant seqera.executor.labels config option (breaking change for plugin nf-seqera, replaced entirely by process.resourceLabels).

This fixes a gap where the process.resourceLabels directive — emitted by AbstractComputePlatformProvider.addConfigResourceLabels() for every CE type and honoured by AWS Batch / GCP Batch / Azure / K8s — was effectively dead on the Seqera Compute path.

Motivation

SeqeraTaskHandler.submit() previously built the scheduler Task with only name, image, command, environment, resourceRequirement, resourceLimit, machineRequirement, and nextflow(taskId/hash/workDir) — it never read task.config.getResourceLabels(). The plugin's only label path was at the run level (seqera.executor.labels + autoLabels), so per-process labels emitted via the standard directive were silently dropped on Seqera Compute while working on every other supported executor.

Cumulative model rationale: per-task scheduler payloads stay small (only the delta is sent); same-key collisions between the config baseline and a per-process override resolve naturally on the scheduler side (task labels override run labels), preserving Nextflow's existing directive semantics.

Changes

Plugin (plugins/nf-seqera)

• Labels.withProcessResourceLabels(Map<String,?>) — new instance method that adds config-level labels to the run-label map, coercing values via String.valueOf to satisfy sched-api's Map<String,String> typing.
• Labels.toStringMap(Map<String,?>) — static helper returning a coerced map (or Collections.emptyMap() for null/empty input).
• Labels.delta(task, run) — static helper returning entries in task that are missing from run or have a different value. Returns null when the result would be empty (so callers can omit the field).
• SeqeraExecutor:
  • new private cached field runResourceLabels (initialised to empty map);
  • new @PackageScope void computeRunResourceLabels() reads session.config.process.resourceLabels and stores the coerced baseline;
  • new public getter getRunResourceLabels();
  • createRun() invokes computeRunResourceLabels() and calls labels.withProcessResourceLabels(runResourceLabels) after the autoLabels block.
• SeqeraTaskHandler.submit() computes Labels.delta(Labels.toStringMap(task.config.getResourceLabels()), executor.runResourceLabels) and attaches it to Task.labels only when non-empty.
• seqera.executor.labels config option, ExecutorOpts.labels field/getter, and Labels.withUserLabels(Map) removed; obsolete tests dropped from ExecutorOptsTest, LabelsTest, and SeqeraConfigTest.
• Plugin VERSION bumped to 0.18.0; changelog.txt updated.
• sched-client bumped to 0.52.0-SNAPSHOT (which exposes Task.labels).

Tests (Spock)

• LabelsTest covers withProcessResourceLabels (coercion, null/empty, override semantics) plus toStringMap and delta (null/empty handling, full-when-empty-baseline, missing/differing-only deltas).
• SeqeraExecutorTest adds:
  • isolated test of computeRunResourceLabels() populating the cached map, including non-String value coercion;
  • end-to-end createRun() test asserting CreateRunRequest.labels contains both the config-level process.resourceLabels entries and the nextflow.io/* auto-label entries when autoLabels is enabled.
• SeqeraTaskHandlerTest:
  • new tests verify submit() attaches Task.labels containing only the delta and leaves Task.labels unset when task labels equal the run baseline;
  • existing Mock(SeqeraExecutor) blocks tightened with getRunResourceLabels() >> [:] to reflect the runtime invariant.

Docs

• docs/reference/process.md adds seqera-executor to the resourceLabels support list.

Breaking change

The seqera.executor.labels config option is removed. Users on plugin nf-seqera 0.17.x must migrate to the standard Nextflow directive:

// before
seqera.executor.labels = [project: 'genomics', team: 'research']

// after
process.resourceLabels = [project: 'genomics', team: 'research']

The directive may be set at the config level (applied to all processes), under withName:/withLabel: selectors, or inside individual process {} bodies — all forms accumulate per Nextflow's normal merging rules. The config-level entries become the run baseline; selector/process-body entries become per-task deltas.

Test plan

• ./gradlew :plugins:nf-seqera:test — green
• Spec coverage cross-checked against the design doc (docs/superpowers/specs/2026-04-17-seqera-resource-labels-design.md)
• CI reruns the full plugin suite after the new sched-client:0.52.0-SNAPSHOT artifact resolves from the published Maven repo
• Smoke run on a real Sched-backed compute env with a workflow that combines a config-level process.resourceLabels baseline plus per-process directives, verifying the resulting run labels and per-task labels in the scheduler

Notes

• Design and implementation plan committed under docs/superpowers/{specs,plans}/2026-04-17-seqera-resource-labels-*.md for review traceability.
• settings.gradle retains an opt-in commented includeBuild '../sched' hint for local development against an unreleased sched-client; CI builds use the published Maven artifact.

[netlify]

✅ Deploy Preview for nextflow-docs-staging ready!

Name	Link
🔨 Latest commit	d083525
🔍 Latest deploy log	https://app.netlify.com/projects/nextflow-docs-staging/deploys/69e6583866697c00096d635c
😎 Deploy Preview	https://deploy-preview-7048--nextflow-docs-staging.netlify.app
📱 Preview on mobile	Toggle QR Code... Use your smartphone camera to open QR code link.

---

To edit notification comments on pull requests, go to your Netlify project configuration.

[bentsherman]

Don't forget to remove seqera.executor.labels from docs/reference/config.md

[pditommaso]

Well spotted, done