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I wonder if we can fold |
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Yeah, this is temporary. We to find a better packing. |
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
…ropagation Wrap cancelTask call in try-catch to prevent exceptions from escaping killTask(). This ensures handleException() is called with the original error, allowing proper workflow termination instead of crashing the task monitor poll loop. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- Add keep-alive mechanism to send empty submissions after 60s idle - Pass sessionId to batch submitter for API calls - Add null check in killTask when taskId not yet assigned - Update sched-client to 0.9.0-SNAPSHOT - Bump plugin version to 0.4.0 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- Define SEQERA constant in SeqeraExecutor for reuse - Override executor name in trace record to 'seqera/aws' for cost tracking - Add unit test for getTraceRecord() method - Remove obsolete convertPriceModel test (moved to MapperUtil) Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
… [ci fast] - Add nf-seqera plugin to packing.gradle and plugins-info.txt - Fix workflow hang when batch submission fails by detecting early failure in checkIfCompleted() Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Add proper error handling to prevent thread crashes and enable graceful workflow abort on fatal errors: - Add onError callback to propagate fatal errors to session - Wrap sendTasks0 loop in try-catch to handle unexpected Throwables - Protect keep-alive calls to prevent thread crash on transient failures - Add drainAndFailPendingTasks helper to notify pending tasks on failure - Update SeqeraExecutor to pass session.abort callback Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
…xit code [ci fast] When a Seqera task fails (status=FAILED) but no exit code is available (exitStatus=MAX_VALUE), set task.error to a ProcessException with the error message from the task state, or a fallback message if not available. This aligns with the error handling pattern used in AWS Batch and Google Batch executors. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
…onfig warnings
The config validator checks @ConfigOption FIRST - if present, it treats
the field as a leaf Option and doesn't recurse into nested ConfigScope
types. This caused spurious warnings for machineRequirement nested options:
WARN: Unrecognized config option 'seqera.machineRequirement.provisioning'
WARN: Unrecognized config option 'seqera.machineRequirement.maxSpotAttempts'
Removing @ConfigOption allows the validator to recognize that
MachineRequirementOpts implements ConfigScope and properly discover
its nested @ConfigOption fields.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Signed-off-by: Lorenzo Fontana <fontanalorenz@gmail.com>
- Add disk configuration options to MachineRequirementOpts (diskType, diskThroughputMiBps, diskIops, diskEncrypted) - Extend DiskResource with cloud-specific properties (iops, throughput, encrypted, filesystem, mountPath) - Add MapperUtil.toDiskRequirement() to map disk settings to sched API - Update sched-client to 0.14.0-SNAPSHOT for DiskRequirement support - Document EBS disk configuration in executor.md and config.md - Default to gp3 volumes with 325 MiB/s throughput (Fusion recommended) Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- Add diskAllocation config option (task/node) to MachineRequirementOpts - Update MapperUtil to map allocation and use correct volumeType API - Add validation: node allocation only supports disk size - Bump sched-client to 0.16.0-SNAPSHOT Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Validate that the container image is not empty before submitting tasks to the Seqera scheduler. The executor requires all processes to specify a container image, so this throws ProcessUnrecoverableException with a clear error message when the container is missing. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Add configurable labels that are propagated to AWS resources (ECS tasks, capacity providers, EC2 instances) for cost tracking and resource organization. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Make ExecutorOpts implement ConfigScope and remove @ConfigOption from the executor field in SeqeraConfig so nested config options are properly discovered by the config validator. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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Looks good enough to merge, just left a few minor suggestions
Co-authored-by: Ben Sherman <bentshermann@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
--------- Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Jon Martí <jmartifraiz@gmail.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io> Co-authored-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> Co-authored-by: Lorenzo Fontana <fontanalorenz@gmail.com>
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* Add Nextflow Development Constitution Introduce comprehensive development constitution documenting core principles and practices for Nextflow development including modular architecture, test-driven quality assurance, dataflow programming model, licensing compliance, DCO requirements, semantic versioning, and Groovy code standards. The constitution codifies existing best practices from CLAUDE.md and CONTRIBUTING.md to provide clear governance and quality standards for the project. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Module adr v1 Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Module adr v2 Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * ADR: Nextflow remote modules system v2.1 Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Add detailed CLI command descriptions to module system ADR [ci skip] - Add comprehensive documentation for all module CLI commands - Add `nextflow module run` command for standalone module execution - Remove `module update` command to simplify the design - Use single-dash prefix for Nextflow options, double-dash for module inputs - Remove @ prefix from scope in CLI commands (keep only in DSL syntax) Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Simplify module spec: unify dependencies under requires - Remove separate `dependencies` and `components` fields - Expand `requires` to include: - `nextflow`: version constraint (unchanged) - `plugins`: array with name@constraint syntax - `modules`: array of module dependencies - `workflows`: array of workflow dependencies - Unified version constraint syntax: `[scope/]name[@constraint]` - Mark `components` as deprecated (use requires.modules) - Update all examples in ADR and schema Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Add structured tool arguments to module spec schema - Add `args` property to tools section for type-safe argument configuration - Define toolArgSpec with flag, type, description, default, enum, required - Support implicit variable `tools.<toolname>.args.<argname>` returning formatted flag+value (e.g., "-K 100000000") - Support `tools.<toolname>.args` to return all args concatenated - Document deprecation of ext.args/ext.args2/ext.args3 pattern - Update ADR with Tool Arguments Configuration section and appendix [ci skip] Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Update adr/20251114-module-system.md [ci skip] Co-authored-by: Jorge Ejarque <jorgee@users.noreply.github.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Update adr/20251114-module-system.md [ci skip] Co-authored-by: Jorge Ejarque <jorgee@users.noreply.github.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Update adr/20251114-module-system.md [ci skip] Co-authored-by: Jorge Ejarque <jorgee@users.noreply.github.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Update adr/20251114-module-system.md [ci skip] Expand deprecation notice to cover all ext.* custom directives Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Fix inconsistencies in module system ADR [ci skip] - Use consistent module path format with version: modules/@scope/name@version/ - Fix directory structure example: samtools-view -> samtools/view - Standardize on 'license' spelling (American English) - Fix author -> authors (plural array format) Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Fix registry API path in comparison table [ci skip] Remove @ prefix from scope in API path to match API definition Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Fix checksum format: sha256- -> sha256: [ci skip] Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Update module API to match registry implementation [ci skip] - Update API endpoints to match seqeralabs/plugin-registry#266 - Use /api/modules base path (no v1 prefix) - Use single {name} parameter with namespace (e.g., "nf-core/fastqc") - Add separate /releases endpoint - Simplify publish to single POST endpoint Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Update adr [ci skip] Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Simplify module storage and verification model [ci skip] - Remove checksums from nextflow.config (registry is source of truth) - Use single version per module locally (no version in directory path) - Add .checksum file in module directory for integrity verification - Simplify freeze command to only pin transitive dependency versions - Checksum mismatch reports warning instead of automatic re-download - Remove resolved open question about checksum verification Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Update adr/20251114-module-system.md [ci skip] Co-authored-by: Jorge Ejarque <jorgee@users.noreply.github.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Clarify module resolution rules for version changes vs local modifications [ci skip] - Added Resolution Rules table clearly specifying behavior for each scenario: - Version change (local unmodified): automatically replace with declared version - Local modification (checksum mismatch): warn and protect local changes - Use -force flag to override locally modified modules - Updated install command behavior to reflect checksum verification - Updated Technical Details with expanded resolution flow Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * ADR v2.3: Fix resolution rules consistency and add version entry [ci skip] - Fixed Resolution Rules table: locally modified modules will NOT be replaced unless -force is used (was incorrectly saying "will be replaced") - Added Version 2.3 changelog entry documenting: - Resolution Rules table with clear behavior matrix - Local modification protection with -force flag - Simplified storage model (single version per module) - .checksum file for fast integrity verification Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Fix Version 2.1 date typo: 2025 -> 2024 [ci skip] Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Add module system client specification [ci skip] Specification for Nextflow module system client implementation based on ADR 20251114-module-system.md. Covers: P1 (Core): - Install and use registry modules via @scope/name syntax - Run modules directly from CLI without wrapper workflow - Structured tool arguments replacing ext.args pattern P2 (Important): - Module version management and freeze command - Module integrity protection with checksum validation P3 (Nice to have): - Remove module command - Search and discover modules - Publish module to registry Registry backend is out of scope (assumed implemented). Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Remove transitive dependency resolution from module system [ci skip] - Remove `freeze` command from CLI - Remove transitive dependency install behavior - Remove orphaned transitive dependency removal from `remove` command - Update rationale and consequences sections - Simplify dependency resolution flow - Update ADR to version 2.4 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Update adr/20251114-module-system.md [ci skip] Co-authored-by: Jorge Ejarque <jorgee@users.noreply.github.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Update adr/20251114-module-system.md [ci skip] Co-authored-by: Phil Ewels <phil.ewels@seqera.io> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Update modules plan [ci skip] Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Remove tools config [ci skip] Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Simplify module system requires definition [ci skip] - Remove plugins, modules, subworkflows from requires block - Spec now focused on process modules only - Dependencies managed via nextflow.config Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Replace tool arguments with module parameters in ADR [ci skip] - Module parameters defined in meta.yaml params section with name, type, description, and example attributes - Removed tools args property and specification - Updated schema and examples throughout Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Update specs + adr [ci skip] Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Resolve some conflicts with nextflow-io/schemas#10 Signed-off-by: Ben Sherman <bentshermann@gmail.com> * Update adr/20251114-module-system.md [ci skip] Co-authored-by: Ben Sherman <bentshermann@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Extract module parameters to separate spec [ci skip] Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * docs: clarify path name for staged task inputs (#6869) Co-authored-by: Ben Sherman <bentshermann@gmail.com> * Add devcontainer (#6792) Co-authored-by: Phil Ewels <phil.ewels@seqera.io> Co-authored-by: Ben Sherman <bentshermann@gmail.com> * Fix vertical alignment in timeline report (#6794) * Ensure main script is first in the WorkflowRun lineage record (#6845) * Add whitespace rules to .editorconfig (#5606) * docs: Update your first script to use outputs (#6500) * Update AWS CLI install docs to bypass conda install TOS prompt (#6685) * Clarify onError and onComplete handler descriptions (#6709) [ci fast] * Use explicit memory units for LSF executor (#5217) Signed-off-by: Ben Sherman <bentshermann@gmail.com> * Treat LSF job status UNKWN as HOLD (#5756) * Allow boolean params to implicitly default to false (#6764) * Sched core implementation alpha1 (#6242) Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> Co-authored-by: Lorenzo Fontana <fontanalorenz@gmail.com> * Revert version 26.01.1-edge Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Bump copyright 2026 Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Handle Azure Batch ActiveJobAndScheduleQuotaReached with retry (#6874) * Handle Azure Batch ActiveJobAndScheduleQuotaReached with retry (#5575) Add retry logic when Azure Batch returns HTTP 409 with ActiveJobAndScheduleQuotaReached error code during job creation, instead of failing immediately. Configurable via azure.batch.maxJobQuotaRetries (default 3) and azure.batch.jobQuotaRetryDelay (default 2 min). Generated by Claude Code Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com> * Refactor job quota retry to use Failsafe RetryPolicy Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> --------- Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com> * [ci fast] Add agent output mode (NXF_AGENT_MODE) Add AI agent-friendly output mode activated via NXF_AGENT_MODE=1. When enabled, Nextflow replaces the interactive ANSI progress display with minimal, structured tagged lines optimized for AI agent context windows: [PIPELINE] name version | profile=X [WORKDIR] /path/to/work [PROCESS hash] name (tag) [WARN] deduplicated warning [ERROR] name with exit/cmd/stderr/workdir [SUCCESS|FAILED] completed=N failed=N cached=N Key changes: - LogObserver interface as common abstraction for AnsiLogObserver and AgentLogObserver - Session holds a single logObserver field instead of two concrete fields - DefaultObserverFactory creates both observer types using the same pattern - AgentLogObserver filters hash-prefixed log lines to avoid duplicating [PROCESS] output - Workflow output (view operator) passes through to stdout in agent mode - Renamed env var from NXF_AGENT to NXF_AGENT_MODE - Added NXF_AGENT_MODE to environment variables documentation * Bump nf-amazon@3.7.1 Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Bump nf-azure@1.22.0 Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Bump nf-google@1.26.1 Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Bump nf-tower@1.21.0 Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Bump nf-seqera@0.12.0 Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Bump nf-tower@1.21.0 nextflowVersion Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Bump nf-seqera@0.12.0 nextflowVersion and README Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Fix AgentLogObserver println clash with Groovy GDK method Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Add Summary section to plugin README files Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * [release] [ci fast] Nextflow version 26.02.0-edge Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Fix docs [ci skip] Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> * Add logStreamId to Tower task record (#6877) Propagate the log stream identifier from TraceRecord to the Tower task record so that Seqera Platform can link tasks to their cloud log streams. Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com> * Don't include container in task trace when containers are not enabled (#6824) * Propagate errors from workflow outputs (#6876) * Fix type detection of CLI params in v2 config parser (#6765) * Add NVMe disk allocation and diskMountPath support (#6879) [ci fast] * Add NVMe disk allocation and diskMountPath support for Seqera executor For task/node allocation the default is /tmp; for nvme allocation the default is the server-configured NVMe mount path (typically /scratch). Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com> * Version 2.7: rename `.checksum` to `.module-info`, remove `@` prefix from module scopes, remove version pinning from `nextflow.config` Signed-off-by: Ben Sherman <bentshermann@gmail.com> * Module System Implementation (#6768) Signed-off-by: jorgee <jorge.ejarque@seqera.io> * minor edits Signed-off-by: Ben Sherman <bentshermann@gmail.com> * Cleanup module run output Signed-off-by: Ben Sherman <bentshermann@gmail.com> * Fix meta.yaml -> meta.yml, module manifest -> module spec Signed-off-by: Ben Sherman <bentshermann@gmail.com> * Fix failing test Signed-off-by: Ben Sherman <bentshermann@gmail.com> * fix tests Signed-off-by: jorgee <jorge.ejarque@seqera.io> * modify module list to skip subdirectories of directories that already contains the .module-info. This folders can't be a module Signed-off-by: jorgee <jorge.ejarque@seqera.io> * Update docs Signed-off-by: Ben Sherman <bentshermann@gmail.com> * Apply suggestion from @pditommaso [ci skip] Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> --------- Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Signed-off-by: Ben Sherman <bentshermann@gmail.com> Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com> Signed-off-by: jorgee <jorge.ejarque@seqera.io> Co-authored-by: Claude <noreply@anthropic.com> Co-authored-by: Jorge Ejarque <jorgee@users.noreply.github.com> Co-authored-by: Phil Ewels <phil.ewels@seqera.io> Co-authored-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Abi <llawlietbagsum@gmail.com> Co-authored-by: Peter Kneale <PeterKneale@gmail.com> Co-authored-by: Chris Hakkaart <chris.hakkaart@seqera.io> Co-authored-by: Rintze Zelle <78232505+rzelle-lallemand@users.noreply.github.com> Co-authored-by: Colin J. Brislawn <cbrisl@gmail.com> Co-authored-by: Lorenzo Fontana <fontanalorenz@gmail.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: jorgee <jorge.ejarque@seqera.io>
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Draft implementation for sched poc