25 KiB
Seqera executor process.resourceLabels Implementation Plan
For agentic workers: REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (
- [ ]) syntax for tracking.
Goal: Make the nf-seqera executor honour process.resourceLabels by sending the config-level baseline as run labels and the per-task delta as Sched task labels.
Architecture: Cumulative Nextflow labels split into two scheduler scopes — config-level process.resourceLabels becomes CreateRunRequest.labels; the difference between task.config.getResourceLabels() and that baseline becomes Task.labels. The redundant seqera.executor.labels config option is removed.
Tech Stack: Groovy 4 / Java 21 toolchain, Gradle, Spock, io.seqera:sched-client (≥ 0.51.0 — must expose Task.labels), Nextflow extension-point plugin model.
Spec: docs/superpowers/specs/2026-04-17-seqera-resource-labels-design.md
File map:
- Modify
settings.gradle— uncomment-styleincludeBuild '../sched'for dev - Modify
plugins/nf-seqera/build.gradle— bumpsched-clientversion - Modify
plugins/nf-seqera/src/main/io/seqera/executor/Labels.groovy— addwithProcessResourceLabels, adddelta, removewithUserLabels - Modify
plugins/nf-seqera/src/main/io/seqera/config/ExecutorOpts.groovy— removelabelsfield - Modify
plugins/nf-seqera/src/main/io/seqera/executor/SeqeraExecutor.groovy— wire run labels + cacherunResourceLabels - Modify
plugins/nf-seqera/src/main/io/seqera/executor/SeqeraTaskHandler.groovy— attach delta toTask.labels - Modify
plugins/nf-seqera/src/test/io/seqera/executor/LabelsTest.groovy - Modify
plugins/nf-seqera/src/test/io/seqera/config/ExecutorOptsTest.groovy - Modify
plugins/nf-seqera/src/test/io/seqera/executor/SeqeraTaskHandlerTest.groovy - Modify
docs/reference/process.md— add Seqera executor to support list - Modify
plugins/nf-seqera/changelog.txt— entry - Modify
plugins/nf-seqera/VERSION— bump to0.18.0
Task 1: Bump sched-client and wire includeBuild '../sched'
Files:
- Modify:
plugins/nf-seqera/build.gradle:54 - Modify:
settings.gradle:17-19
The local ~/Projects/sched checkout is at 0.51.0; that is the version exposing Task.labels. Until 0.51.0 is published to the Seqera Maven repo, we use a Gradle composite build to substitute the dependency from the local checkout.
- Step 1: Bump sched-client version
Edit plugins/nf-seqera/build.gradle:54:
api 'io.seqera:sched-client:0.51.0'
- Step 2: Add
includeBuild '../sched'block tosettings.gradle
Replace the commented pluginManagement block at settings.gradle:17-19 with both blocks (keep the existing comment, add a new one for sched as dev-only opt-in):
// pluginManagement {
// includeBuild '../nextflow-plugin-gradle'
// }
// For local development against an unpublished sched-client, uncomment:
// includeBuild '../sched'
includeBuild '../sched'
(The uncommented includeBuild '../sched' line is required for the build to resolve sched-client:0.51.0 until the artifact is published. The commented hint stays for future reference.)
- Step 3: Verify the build resolves
Run: ./gradlew :plugins:nf-seqera:compileGroovy
Expected: BUILD SUCCESSFUL. If it fails with a missing sched-client:0.51.0, confirm ~/Projects/sched/VERSION contains 0.51.0 and that ~/Projects/sched/sched-client builds locally (cd ~/Projects/sched && ./gradlew :sched-client:assemble).
- Step 4: Commit
git add settings.gradle plugins/nf-seqera/build.gradle
git commit -s -m "build(nf-seqera): bump sched-client to 0.51.0 via includeBuild"
Task 2: Add Labels.withProcessResourceLabels (TDD)
Files:
-
Modify:
plugins/nf-seqera/src/main/io/seqera/executor/Labels.groovy -
Modify:
plugins/nf-seqera/src/test/io/seqera/executor/LabelsTest.groovy -
Step 1: Write the failing tests
Append to plugins/nf-seqera/src/test/io/seqera/executor/LabelsTest.groovy (before the closing }):
def 'should add process resource labels coercing values to string'() {
when:
def labels = new Labels()
.withProcessResourceLabels([team: 'genomics', priority: 7, retain: true])
then:
labels.entries['team'] == 'genomics'
labels.entries['priority'] == '7'
labels.entries['retain'] == 'true'
}
def 'should ignore null or empty process resource labels'() {
when:
def a = new Labels().withProcessResourceLabels(null)
def b = new Labels().withProcessResourceLabels([:])
then:
a.entries.isEmpty()
b.entries.isEmpty()
}
def 'should let process resource labels override workflow metadata on key collision'() {
given:
def workflow = Mock(WorkflowMetadata) {
getProjectName() >> 'hello'
getRunName() >> 'happy_turing'
getSessionId() >> UUID.randomUUID()
isResume() >> false
getManifest() >> new Manifest([:])
}
when:
def labels = new Labels()
.withWorkflowMetadata(workflow)
.withProcessResourceLabels(['nextflow.io/runName': 'custom', team: 'a'])
then:
labels.entries['nextflow.io/runName'] == 'custom'
labels.entries['team'] == 'a'
labels.entries['nextflow.io/projectName'] == 'hello'
}
- Step 2: Run the tests to verify they fail
Run: ./gradlew :plugins:nf-seqera:test --tests 'io.seqera.executor.LabelsTest' -i
Expected: FAIL — MissingMethodException: No signature of method ... withProcessResourceLabels.
- Step 3: Implement
withProcessResourceLabels
Edit plugins/nf-seqera/src/main/io/seqera/executor/Labels.groovy. After the withUserLabels method (which will be removed in Task 4), add:
/**
* Add config-level {@code process.resourceLabels}. Values are coerced to
* string via {@link String#valueOf} to satisfy the scheduler API typing.
*/
Labels withProcessResourceLabels(Map<String,?> map) {
if( !map ) return this
map.each { k, v -> entries.put(k.toString(), String.valueOf(v)) }
return this
}
- Step 4: Run the tests to verify they pass
Run: ./gradlew :plugins:nf-seqera:test --tests 'io.seqera.executor.LabelsTest' -i
Expected: PASS for the three new tests; existing tests still PASS.
- Step 5: Commit
git add plugins/nf-seqera/src/main/io/seqera/executor/Labels.groovy \
plugins/nf-seqera/src/test/io/seqera/executor/LabelsTest.groovy
git commit -s -m "feat(nf-seqera): add Labels.withProcessResourceLabels"
Task 3: Add Labels.delta and Labels.toStringMap helpers (TDD)
Files:
- Modify:
plugins/nf-seqera/src/main/io/seqera/executor/Labels.groovy - Modify:
plugins/nf-seqera/src/test/io/seqera/executor/LabelsTest.groovy
These two static helpers compute the per-task delta and coerce arbitrary Map<String,?> values to strings — used by both the executor (to cache the run baseline) and the task handler (to compute the delta).
- Step 1: Write the failing tests
Append to plugins/nf-seqera/src/test/io/seqera/executor/LabelsTest.groovy (before the closing }):
def 'should coerce map values to strings'() {
expect:
Labels.toStringMap(null) == [:]
Labels.toStringMap([:]) == [:]
Labels.toStringMap([a: 1, b: 'x', c: true]) == [a: '1', b: 'x', c: 'true']
}
def 'should compute null delta when task labels are empty'() {
expect:
Labels.delta(null, [team: 'a']) == null
Labels.delta([:], [team: 'a']) == null
}
def 'should return full task labels when run labels are empty'() {
expect:
Labels.delta([team: 'a', region: 'us'], null) == [team: 'a', region: 'us']
Labels.delta([team: 'a', region: 'us'], [:]) == [team: 'a', region: 'us']
}
def 'should keep only differing or missing keys in delta'() {
expect:
Labels.delta([team: 'a', region: 'us'], [team: 'a']) == [region: 'us']
Labels.delta([team: 'b'], [team: 'a']) == [team: 'b']
Labels.delta([team: 'a', region: 'us'], [team: 'a', region: 'us']) == null
}
- Step 2: Run the tests to verify they fail
Run: ./gradlew :plugins:nf-seqera:test --tests 'io.seqera.executor.LabelsTest' -i
Expected: FAIL — MissingMethodException: ... toStringMap and ... delta.
- Step 3: Implement the helpers
Edit plugins/nf-seqera/src/main/io/seqera/executor/Labels.groovy. Inside the class, after the existing runId method, add:
/**
* Coerce arbitrary map values to strings via {@link String#valueOf}.
* Returns an empty map for null/empty input.
*/
static Map<String,String> toStringMap(Map<String,?> map) {
if( !map ) return Collections.<String,String>emptyMap()
final result = new LinkedHashMap<String,String>(map.size())
map.each { k, v -> result.put(k.toString(), String.valueOf(v)) }
return result
}
/**
* Return the entries of {@code task} that are missing from {@code run}
* or have a different value. Returns {@code null} if the resulting
* map would be empty (so callers can omit the field).
*/
static Map<String,String> delta(Map<String,String> task, Map<String,String> run) {
if( !task ) return null
final result = new LinkedHashMap<String,String>()
task.each { k, v ->
if( run == null || !run.containsKey(k) || run.get(k) != v )
result.put(k, v)
}
return result.isEmpty() ? null : result
}
- Step 4: Run the tests to verify they pass
Run: ./gradlew :plugins:nf-seqera:test --tests 'io.seqera.executor.LabelsTest' -i
Expected: PASS for all new tests; existing tests still PASS.
- Step 5: Commit
git add plugins/nf-seqera/src/main/io/seqera/executor/Labels.groovy \
plugins/nf-seqera/src/test/io/seqera/executor/LabelsTest.groovy
git commit -s -m "feat(nf-seqera): add Labels.toStringMap and Labels.delta helpers"
Task 4: Remove seqera.executor.labels config option
Files:
- Modify:
plugins/nf-seqera/src/main/io/seqera/config/ExecutorOpts.groovy:74-79,130,168-170 - Modify:
plugins/nf-seqera/src/main/io/seqera/executor/Labels.groovy:81-88 - Modify:
plugins/nf-seqera/src/main/io/seqera/executor/SeqeraExecutor.groovy:120 - Modify:
plugins/nf-seqera/src/test/io/seqera/config/ExecutorOptsTest.groovy:131-165 - Modify:
plugins/nf-seqera/src/test/io/seqera/executor/LabelsTest.groovy:127-150,192-199
The user-facing seqera.executor.labels option is replaced by the standard Nextflow process.resourceLabels directive.
- Step 1: Remove the field and getter from
ExecutorOpts
Edit plugins/nf-seqera/src/main/io/seqera/config/ExecutorOpts.groovy:
Remove lines 74-79 (the @ConfigOption block and final Map<String, String> labels field):
@ConfigOption
@Description("""
Custom labels to apply to AWS resources for cost tracking and resource organization.
Labels are propagated to ECS tasks, capacity providers, and EC2 instances.
""")
final Map<String, String> labels
Remove the assignment in the constructor (around line 129-130):
// labels for cost tracking
this.labels = opts.labels as Map<String, String>
Remove the getter (around line 168-170):
Map<String, String> getLabels() {
return labels
}
- Step 2: Remove the
withUserLabelsmethod fromLabels
Edit plugins/nf-seqera/src/main/io/seqera/executor/Labels.groovy. Delete the entire withUserLabels method (lines 81-88):
/**
* Add user-configured labels. These take precedence over implicit labels.
*/
Labels withUserLabels(Map<String,String> labels) {
if( labels )
entries.putAll(labels)
return this
}
- Step 3: Remove the
withUserLabelscall site inSeqeraExecutor.createRun()
Edit plugins/nf-seqera/src/main/io/seqera/executor/SeqeraExecutor.groovy. Delete the line:
labels.withUserLabels(seqeraConfig.labels)
- Step 4: Remove obsolete tests
Edit plugins/nf-seqera/src/test/io/seqera/config/ExecutorOptsTest.groovy. Delete the three tests (lines 131-165): 'should create config with labels', 'should handle null labels', 'should handle empty labels'.
Edit plugins/nf-seqera/src/test/io/seqera/executor/LabelsTest.groovy. Delete the two tests: 'should allow user labels to override implicit labels' (lines 127-150) and 'should handle null user labels' (lines 192-199).
- Step 5: Compile and run tests
Run: ./gradlew :plugins:nf-seqera:compileGroovy :plugins:nf-seqera:test
Expected: BUILD SUCCESSFUL; all remaining tests PASS. If the compiler complains about a stray reference to seqeraConfig.labels or withUserLabels, grep for and remove them: rg "seqeraConfig\.labels|withUserLabels" plugins/nf-seqera.
- Step 6: Commit
git add plugins/nf-seqera/src/main/io/seqera/config/ExecutorOpts.groovy \
plugins/nf-seqera/src/main/io/seqera/executor/Labels.groovy \
plugins/nf-seqera/src/main/io/seqera/executor/SeqeraExecutor.groovy \
plugins/nf-seqera/src/test/io/seqera/config/ExecutorOptsTest.groovy \
plugins/nf-seqera/src/test/io/seqera/executor/LabelsTest.groovy
git commit -s -m "refactor(nf-seqera)!: remove seqera.executor.labels in favour of process.resourceLabels"
Task 5: Wire process.resourceLabels into SeqeraExecutor.createRun() and expose runResourceLabels (TDD)
Files:
- Modify:
plugins/nf-seqera/src/main/io/seqera/executor/SeqeraExecutor.groovy - Modify:
plugins/nf-seqera/src/test/io/seqera/executor/SeqeraExecutorTest.groovy
The executor reads the config-level process.resourceLabels map once at run creation, attaches it to the run labels via Labels.withProcessResourceLabels, and caches the coerced map so task handlers can compute deltas.
- Step 1: Write the failing test
Append to plugins/nf-seqera/src/test/io/seqera/executor/SeqeraExecutorTest.groovy (before the final closing }):
def 'should expose run resource labels coerced from config-level process.resourceLabels'() {
given:
def executor = new SeqeraExecutor()
executor.@session = Mock(Session) {
getConfig() >> [process: [resourceLabels: [team: 'a', priority: 7]]]
}
when:
executor.computeRunResourceLabels()
then:
executor.runResourceLabels == [team: 'a', priority: '7']
}
def 'should yield empty run resource labels when process.resourceLabels is absent'() {
given:
def executor = new SeqeraExecutor()
executor.@session = Mock(Session) {
getConfig() >> [:]
}
when:
executor.computeRunResourceLabels()
then:
executor.runResourceLabels == [:]
}
(Session is already imported at line 21; if not, add the import.)
- Step 2: Run the test to verify it fails
Run: ./gradlew :plugins:nf-seqera:test --tests 'io.seqera.executor.SeqeraExecutorTest' -i
Expected: FAIL — computeRunResourceLabels / runResourceLabels don't exist.
- Step 3: Implement on
SeqeraExecutor
Edit plugins/nf-seqera/src/main/io/seqera/executor/SeqeraExecutor.groovy.
Add a private field near the other private fields (after runId at line 65):
private volatile Map<String,String> runResourceLabels = Collections.<String,String>emptyMap()
Add a method to compute the run resource labels (place near other protected/package methods, e.g. before createRun() at line 110):
@groovy.transform.PackageScope
void computeRunResourceLabels() {
final processMap = session.config.process as Map
final raw = processMap?.get('resourceLabels') as Map<String,?>
this.runResourceLabels = Labels.toStringMap(raw)
}
Add the public getter (after getRunId() around line 204):
Map<String,String> getRunResourceLabels() {
return runResourceLabels
}
Wire it into createRun(). Replace the labels-building block at SeqeraExecutor.groovy:117-120 (after the deletion in Task 4 it should look like the first three lines below) with:
computeRunResourceLabels()
final labels = new Labels()
if( seqeraConfig.autoLabels )
labels.withWorkflowMetadata(session.workflowMetadata)
labels.withProcessResourceLabels(runResourceLabels)
- Step 4: Run the test to verify it passes
Run: ./gradlew :plugins:nf-seqera:test --tests 'io.seqera.executor.SeqeraExecutorTest' -i
Expected: PASS for both new tests; existing tests still PASS.
- Step 5: Commit
git add plugins/nf-seqera/src/main/io/seqera/executor/SeqeraExecutor.groovy \
plugins/nf-seqera/src/test/io/seqera/executor/SeqeraExecutorTest.groovy
git commit -s -m "feat(nf-seqera): attach process.resourceLabels to Sched run labels"
Task 6: Send per-task delta on Task.labels from SeqeraTaskHandler.submit() (TDD)
Files:
- Modify:
plugins/nf-seqera/src/main/io/seqera/executor/SeqeraTaskHandler.groovy - Modify:
plugins/nf-seqera/src/test/io/seqera/executor/SeqeraTaskHandlerTest.groovy
Capture the Task passed to the batch submitter and assert its labels field reflects the delta between the task's getResourceLabels() and the executor's runResourceLabels.
- Step 1: Write the failing tests
Append to plugins/nf-seqera/src/test/io/seqera/executor/SeqeraTaskHandlerTest.groovy (before the final closing }):
def 'submit attaches Task.labels containing only the per-task delta'() {
given:
Task captured = null
def batchSubmitter = Mock(SeqeraBatchSubmitter) {
submit(_, _) >> { args -> captured = args[1] as Task }
}
def taskConfig = Mock(TaskConfig) {
getCpus() >> 2
getMemory() >> MemoryUnit.of('1 GB')
getAccelerator() >> null
getResourceLabels() >> [team: 'a', region: 'us-east-1']
getResourceLimit('memory') >> null
getResourceLimit('cpus') >> null
getDisk() >> null
}
def taskRun = Mock(TaskRun) {
getConfig() >> taskConfig
getWorkDir() >> Paths.get('/work/ab/cd1234')
getWorkDirStr() >> '/work/ab/cd1234'
getContainer() >> 'docker.io/library/alpine:3'
getContainerPlatform() >> 'linux/amd64'
getId() >> TaskId.of(1)
getHash() >> HashCode.fromInt(1)
lazyName() >> 'sample_task'
}
def executor = Mock(SeqeraExecutor) {
getClient() >> Mock(SchedClient)
getBatchSubmitter() >> batchSubmitter
getSeqeraConfig() >> Mock(ExecutorOpts) {
getMachineRequirement() >> Mock(io.seqera.config.MachineRequirementOpts)
getTaskEnvironment() >> [:]
}
getRunResourceLabels() >> [team: 'a']
ensureRunCreated() >> {}
}
def handler = Spy(new SeqeraTaskHandler(taskRun, executor)) {
fusionEnabled() >> true
fusionLauncher() >> Mock(nextflow.fusion.FusionScriptLauncher) {
fusionEnv() >> [:]
}
fusionSubmitCli() >> ['/bin/sh', '-c', 'true']
fusionConfig() >> Mock(nextflow.fusion.FusionConfig) {
snapshotsEnabled() >> false
}
}
when:
handler.submit()
then:
captured != null
captured.getLabels() == [region: 'us-east-1']
}
def 'submit leaves Task.labels unset when the task labels equal the run baseline'() {
given:
Task captured = null
def batchSubmitter = Mock(SeqeraBatchSubmitter) {
submit(_, _) >> { args -> captured = args[1] as Task }
}
def taskConfig = Mock(TaskConfig) {
getCpus() >> 2
getMemory() >> MemoryUnit.of('1 GB')
getAccelerator() >> null
getResourceLabels() >> [team: 'a']
getResourceLimit('memory') >> null
getResourceLimit('cpus') >> null
getDisk() >> null
}
def taskRun = Mock(TaskRun) {
getConfig() >> taskConfig
getWorkDir() >> Paths.get('/work/ab/cd1234')
getWorkDirStr() >> '/work/ab/cd1234'
getContainer() >> 'docker.io/library/alpine:3'
getContainerPlatform() >> 'linux/amd64'
getId() >> TaskId.of(1)
getHash() >> HashCode.fromInt(1)
lazyName() >> 'sample_task'
}
def executor = Mock(SeqeraExecutor) {
getClient() >> Mock(SchedClient)
getBatchSubmitter() >> batchSubmitter
getSeqeraConfig() >> Mock(ExecutorOpts) {
getMachineRequirement() >> Mock(io.seqera.config.MachineRequirementOpts)
getTaskEnvironment() >> [:]
}
getRunResourceLabels() >> [team: 'a']
ensureRunCreated() >> {}
}
def handler = Spy(new SeqeraTaskHandler(taskRun, executor)) {
fusionEnabled() >> true
fusionLauncher() >> Mock(nextflow.fusion.FusionScriptLauncher) {
fusionEnv() >> [:]
}
fusionSubmitCli() >> ['/bin/sh', '-c', 'true']
fusionConfig() >> Mock(nextflow.fusion.FusionConfig) {
snapshotsEnabled() >> false
}
}
when:
handler.submit()
then:
captured != null
captured.getLabels() == null
}
- Step 2: Run the tests to verify they fail
Run: ./gradlew :plugins:nf-seqera:test --tests 'io.seqera.executor.SeqeraTaskHandlerTest' -i
Expected: FAIL — assertions on captured.getLabels() fail because submit() does not set them.
- Step 3: Wire the delta into
submit()
Edit plugins/nf-seqera/src/main/io/seqera/executor/SeqeraTaskHandler.groovy. After the final schedTask = new Task() ... .nextflow(...) block ending around line 140, before the log.debug call at line 141, insert:
// attach per-task resource labels delta (over run-level baseline)
final taskLabels = Labels.toStringMap(task.config.getResourceLabels())
final delta = Labels.delta(taskLabels, executor.runResourceLabels)
if( delta )
schedTask.labels(delta)
- Step 4: Run the tests to verify they pass
Run: ./gradlew :plugins:nf-seqera:test --tests 'io.seqera.executor.SeqeraTaskHandlerTest' -i
Expected: PASS for both new tests; existing tests still PASS.
- Step 5: Run the full plugin test suite
Run: ./gradlew :plugins:nf-seqera:test
Expected: BUILD SUCCESSFUL; no regressions.
- Step 6: Commit
git add plugins/nf-seqera/src/main/io/seqera/executor/SeqeraTaskHandler.groovy \
plugins/nf-seqera/src/test/io/seqera/executor/SeqeraTaskHandlerTest.groovy
git commit -s -m "feat(nf-seqera): send per-task resourceLabels delta on Sched task"
Task 7: Docs, changelog, and version bump
Files:
-
Modify:
docs/reference/process.md:1388-1393 -
Modify:
plugins/nf-seqera/changelog.txt -
Modify:
plugins/nf-seqera/VERSION -
Step 1: Update docs
Edit docs/reference/process.md. Replace the executor support list at lines 1388-1393:
Resource labels are currently supported by the following executors:
- {ref}`awsbatch-executor`
- {ref}`azurebatch-executor`
- {ref}`google-batch-executor`
- {ref}`k8s-executor`
- {ref}`seqera-executor`
(If seqera-executor is not a defined ref, drop the {ref} wrapper and write Seqera executor as plain text.)
- Step 2: Update plugin changelog
Edit plugins/nf-seqera/changelog.txt. Add a new entry at the top, above the 0.17.0 block:
0.18.0 - <today's date>
- Support process.resourceLabels: config-level labels attached to Sched run, per-task delta attached to Sched task
- Remove seqera.executor.labels config option (use process.resourceLabels instead)
- Bump sched-client@0.51.0
- Step 3: Bump plugin VERSION
Edit plugins/nf-seqera/VERSION:
0.18.0
- Step 4: Verify everything builds
Run: ./gradlew :plugins:nf-seqera:check
Expected: BUILD SUCCESSFUL.
- Step 5: Commit
git add docs/reference/process.md plugins/nf-seqera/changelog.txt plugins/nf-seqera/VERSION
git commit -s -m "docs(nf-seqera): document resourceLabels support and bump to 0.18.0"
Self-review checklist (executed)
- Spec coverage: every section of
2026-04-17-seqera-resource-labels-design.mdmaps to a task — sched-client bump (Task 1),withProcessResourceLabels(Task 2),delta+toStringMap(Task 3), removal ofseqera.executor.labels(Task 4), run-level wiring +runResourceLabels(Task 5), per-task delta onTask.labels(Task 6), docs / changelog / VERSION (Task 7). - Placeholder scan: no TBDs, no "implement later", every code step has the actual code.
- Type consistency:
Labels.toStringMap(Map<String,?>)andLabels.delta(Map<String,String>, Map<String,String>)referenced consistently in Tasks 3, 5, 6;runResourceLabelsfield,computeRunResourceLabels()method, andgetRunResourceLabels()getter consistent across Tasks 5 and 6.