# Class: WorkflowEngineConfig _Execution directives for a workflow engine. Every field is optional and each engine's emitter consumes the subset it supports, so one block may carry directives for more than one target. The generic resource fields (cpus_per_task, mem, time) map across engines; the remaining fields are named for the engine that reads them (Slurm: partition/account/gres/ mail_*/array_chunk; Snakemake: cores; Nextflow: executor/queue). Any directive not named here is passed through ``options`` verbatim, so the block stays extensible without a schema change._
URI: [tvbo:WorkflowEngineConfig](https://w3id.org/tvbo/WorkflowEngineConfig) ```{mermaid} classDiagram class WorkflowEngineConfig click WorkflowEngineConfig href "./WorkflowEngineConfig.html" WorkflowEngineConfig : account WorkflowEngineConfig --> "0..1" String : account click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : array_chunk WorkflowEngineConfig --> "0..1" Integer : array_chunk click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html" WorkflowEngineConfig : comment WorkflowEngineConfig --> "0..1" String : comment click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : cores WorkflowEngineConfig --> "0..1" Integer : cores click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html" WorkflowEngineConfig : cpus_per_task WorkflowEngineConfig --> "0..1" Integer : cpus_per_task click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html" WorkflowEngineConfig : env WorkflowEngineConfig --> "*" EnvironmentVariable : env click EnvironmentVariable href "./EnvironmentVariable.html" WorkflowEngineConfig : executor WorkflowEngineConfig --> "0..1" String : executor click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : gres WorkflowEngineConfig --> "0..1" String : gres click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : jobs WorkflowEngineConfig --> "0..1" Integer : jobs click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html" WorkflowEngineConfig : mail_type WorkflowEngineConfig --> "0..1" String : mail_type click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : mail_user WorkflowEngineConfig --> "0..1" String : mail_user click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : mem WorkflowEngineConfig --> "0..1" String : mem click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : modules WorkflowEngineConfig --> "*" String : modules click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : options WorkflowEngineConfig --> "*" SchedulerDirective : options click SchedulerDirective href "./SchedulerDirective.html" WorkflowEngineConfig : partition WorkflowEngineConfig --> "0..1" String : partition click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : queue WorkflowEngineConfig --> "0..1" String : queue click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : setup WorkflowEngineConfig --> "*" String : setup click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : time WorkflowEngineConfig --> "0..1" String : time click String href "../http://www.w3.org/2001/XMLSchema#string.html" WorkflowEngineConfig : venv WorkflowEngineConfig --> "0..1" String : venv click String href "../http://www.w3.org/2001/XMLSchema#string.html" ``` ## Class Properties | Property | Value | | --- | --- | | Class URI | [tvbo:WorkflowEngineConfig](https://w3id.org/tvbo/WorkflowEngineConfig) | ## Slots | Name | Cardinality and Range | Description | Inheritance | | --- | --- | --- | --- | | [cpus_per_task](../slots/cpus_per_task.qmd) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | CPU cores requested per task (Slurm --cpus-per-task) | direct | | [mem](../slots/mem.qmd) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Memory per task in scheduler syntax (e | direct | | [time](../slots/time.qmd) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Wall-clock limit per task (e | direct | | [gres](../slots/gres.qmd) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Generic scheduler resources, e | direct | | [partition](../slots/partition.qmd) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Scheduler partition to submit to (Slurm) | direct | | [account](../slots/account.qmd) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Accounting allocation to charge the tasks against (Slurm) | direct | | [comment](../slots/comment.qmd) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Free-text provenance tag on each submitted job (Slurm ``--comment``), visible... | direct | | [cores](../slots/cores.qmd) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Total cores for local engines (Snakemake --cores) | direct | | [jobs](../slots/jobs.qmd) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Concurrent jobs the workflow engine keeps in flight (Snakemake ``--jobs``, wr... | direct | | [executor](../slots/executor.qmd) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Executor to run the pipeline through (Nextflow process | direct | | [queue](../slots/queue.qmd) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Scheduler queue for the executor (Nextflow process | direct | | [modules](../slots/modules.qmd) | *
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Environment modules to load before running (module load …) | direct | | [venv](../slots/venv.qmd) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Path to a virtual environment to activate before running | direct | | [setup](../slots/setup.qmd) | *
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Shell lines run verbatim before the task command, after ``set -euo pipefail``... | direct | | [mail_type](../slots/mail_type.qmd) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Scheduler notification trigger (e | direct | | [mail_user](../slots/mail_user.qmd) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Notification email address | direct | | [array_chunk](../slots/array_chunk.qmd) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Overrides ``distribute | direct | | [options](../slots/options.qmd) | *
[SchedulerDirective](../classes/SchedulerDirective.qmd) | Additional engine-native scheduler directives passed through verbatim, each i... | direct | | [env](../slots/env.qmd) | *
[EnvironmentVariable](../classes/EnvironmentVariable.qmd) | Environment variables exported before the task command on every engine (e | direct | ## Usages | used by | used in | type | used | | --- | --- | --- | --- | | [WorkflowConfig](../classes/WorkflowConfig.qmd) | [slurm](../slots/slurm.qmd) | range | [WorkflowEngineConfig](../classes/WorkflowEngineConfig.qmd) | | [WorkflowConfig](../classes/WorkflowConfig.qmd) | [snakemake](../slots/snakemake.qmd) | range | [WorkflowEngineConfig](../classes/WorkflowEngineConfig.qmd) | | [WorkflowConfig](../classes/WorkflowConfig.qmd) | [nextflow](../slots/nextflow.qmd) | range | [WorkflowEngineConfig](../classes/WorkflowEngineConfig.qmd) | ## Identifier and Mapping Information ### Schema Source * from schema: https://w3id.org/tvbo ## Mappings | Mapping Type | Mapped Value | | --- | --- | | self | tvbo:WorkflowEngineConfig | | native | tvbo:WorkflowEngineConfig | ## LinkML Source ### Direct
```yaml name: WorkflowEngineConfig description: 'Execution directives for a workflow engine. Every field is optional and each engine''s emitter consumes the subset it supports, so one block may carry directives for more than one target. The generic resource fields (cpus_per_task, mem, time) map across engines; the remaining fields are named for the engine that reads them (Slurm: partition/account/gres/ mail_*/array_chunk; Snakemake: cores; Nextflow: executor/queue). Any directive not named here is passed through ``options`` verbatim, so the block stays extensible without a schema change.' from_schema: https://w3id.org/tvbo attributes: cpus_per_task: name: cpus_per_task description: CPU cores requested per task (Slurm --cpus-per-task). from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: integer minimum_value: 1 mem: name: mem description: Memory per task in scheduler syntax (e.g. '16G'). from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: string time: name: time description: Wall-clock limit per task (e.g. '24:00:00'). from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig - TimeSeries range: string gres: name: gres description: Generic scheduler resources, e.g. 'gpu:1' (Slurm --gres). from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: string partition: name: partition description: Scheduler partition to submit to (Slurm). from_schema: https://w3id.org/tvbo domain_of: - Observation - WorkflowEngineConfig range: string account: name: account description: Accounting allocation to charge the tasks against (Slurm). from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: string comment: name: comment description: Free-text provenance tag on each submitted job (Slurm ``--comment``), visible in ``squeue -o %k``. Unset means an auto-generated ``tvbo:/exp_`` tag so a queued job maps back to its experiment; set it to override with a custom string. from_schema: https://w3id.org/tvbo domain_of: - Parameter - WorkflowEngineConfig range: string cores: name: cores description: Total cores for local engines (Snakemake --cores). from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: integer minimum_value: 1 jobs: name: jobs description: Concurrent jobs the workflow engine keeps in flight (Snakemake ``--jobs``, written into the emitted profile). A site's queue limit is a property of the run, so it belongs beside partition and account; unset means 100. from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: integer minimum_value: 1 executor: name: executor description: Executor to run the pipeline through (Nextflow process.executor). from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: string queue: name: queue description: Scheduler queue for the executor (Nextflow process.queue). from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: string modules: name: modules description: Environment modules to load before running (module load …). from_schema: https://w3id.org/tvbo domain_of: - SoftwareRequirement - WorkflowEngineConfig range: string multivalued: true venv: name: venv description: Path to a virtual environment to activate before running. from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: string setup: name: setup description: Shell lines run verbatim before the task command, after ``set -euo pipefail`` and any module/venv activation. The general hook for environment setup the typed fields do not cover, e.g. activating a conda env (``conda activate ``), sourcing a profile, or exporting a computed path. Ordered; each line is emitted as-is. from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: string multivalued: true mail_type: name: mail_type description: Scheduler notification trigger (e.g. 'END,FAIL'). from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: string mail_user: name: mail_user description: Notification email address. from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: string array_chunk: name: array_chunk description: 'Overrides ``distribute.chunk`` for this engine only: the number of array-task shards to split the vectorized sweep across.' from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: integer minimum_value: 1 options: name: options description: 'Additional engine-native scheduler directives passed through verbatim, each in the target''s native form: a Slurm ``#SBATCH --=`` line, a Snakemake ``resources:`` entry, or a Nextflow ``process.`` assignment. The extension point for any flag the typed fields do not cover.' from_schema: https://w3id.org/tvbo domain_of: - Discretization - BranchSwitch - Continuation - WorkflowEngineConfig range: SchedulerDirective multivalued: true inlined: true inlined_as_list: true env: name: env description: Environment variables exported before the task command on every engine (e.g. XLA_PYTHON_CLIENT_PREALLOCATE=false). An ordered list of {name, value}; values are shell-quoted at emit time. from_schema: https://w3id.org/tvbo rank: 1000 domain_of: - WorkflowEngineConfig range: EnvironmentVariable multivalued: true inlined: true inlined_as_list: true class_uri: tvbo:WorkflowEngineConfig ```
### Induced
```yaml name: WorkflowEngineConfig description: 'Execution directives for a workflow engine. Every field is optional and each engine''s emitter consumes the subset it supports, so one block may carry directives for more than one target. The generic resource fields (cpus_per_task, mem, time) map across engines; the remaining fields are named for the engine that reads them (Slurm: partition/account/gres/ mail_*/array_chunk; Snakemake: cores; Nextflow: executor/queue). Any directive not named here is passed through ``options`` verbatim, so the block stays extensible without a schema change.' from_schema: https://w3id.org/tvbo attributes: cpus_per_task: name: cpus_per_task description: CPU cores requested per task (Slurm --cpus-per-task). from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: integer minimum_value: 1 mem: name: mem description: Memory per task in scheduler syntax (e.g. '16G'). from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: string time: name: time description: Wall-clock limit per task (e.g. '24:00:00'). from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig - TimeSeries range: string gres: name: gres description: Generic scheduler resources, e.g. 'gpu:1' (Slurm --gres). from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: string partition: name: partition description: Scheduler partition to submit to (Slurm). from_schema: https://w3id.org/tvbo owner: WorkflowEngineConfig domain_of: - Observation - WorkflowEngineConfig range: string account: name: account description: Accounting allocation to charge the tasks against (Slurm). from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: string comment: name: comment description: Free-text provenance tag on each submitted job (Slurm ``--comment``), visible in ``squeue -o %k``. Unset means an auto-generated ``tvbo:/exp_`` tag so a queued job maps back to its experiment; set it to override with a custom string. from_schema: https://w3id.org/tvbo owner: WorkflowEngineConfig domain_of: - Parameter - WorkflowEngineConfig range: string cores: name: cores description: Total cores for local engines (Snakemake --cores). from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: integer minimum_value: 1 jobs: name: jobs description: Concurrent jobs the workflow engine keeps in flight (Snakemake ``--jobs``, written into the emitted profile). A site's queue limit is a property of the run, so it belongs beside partition and account; unset means 100. from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: integer minimum_value: 1 executor: name: executor description: Executor to run the pipeline through (Nextflow process.executor). from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: string queue: name: queue description: Scheduler queue for the executor (Nextflow process.queue). from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: string modules: name: modules description: Environment modules to load before running (module load …). from_schema: https://w3id.org/tvbo owner: WorkflowEngineConfig domain_of: - SoftwareRequirement - WorkflowEngineConfig range: string multivalued: true venv: name: venv description: Path to a virtual environment to activate before running. from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: string setup: name: setup description: Shell lines run verbatim before the task command, after ``set -euo pipefail`` and any module/venv activation. The general hook for environment setup the typed fields do not cover, e.g. activating a conda env (``conda activate ``), sourcing a profile, or exporting a computed path. Ordered; each line is emitted as-is. from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: string multivalued: true mail_type: name: mail_type description: Scheduler notification trigger (e.g. 'END,FAIL'). from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: string mail_user: name: mail_user description: Notification email address. from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: string array_chunk: name: array_chunk description: 'Overrides ``distribute.chunk`` for this engine only: the number of array-task shards to split the vectorized sweep across.' from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: integer minimum_value: 1 options: name: options description: 'Additional engine-native scheduler directives passed through verbatim, each in the target''s native form: a Slurm ``#SBATCH --=`` line, a Snakemake ``resources:`` entry, or a Nextflow ``process.`` assignment. The extension point for any flag the typed fields do not cover.' from_schema: https://w3id.org/tvbo owner: WorkflowEngineConfig domain_of: - Discretization - BranchSwitch - Continuation - WorkflowEngineConfig range: SchedulerDirective multivalued: true inlined: true inlined_as_list: true env: name: env description: Environment variables exported before the task command on every engine (e.g. XLA_PYTHON_CLIENT_PREALLOCATE=false). An ordered list of {name, value}; values are shell-quoted at emit time. from_schema: https://w3id.org/tvbo rank: 1000 owner: WorkflowEngineConfig domain_of: - WorkflowEngineConfig range: EnvironmentVariable multivalued: true inlined: true inlined_as_list: true class_uri: tvbo:WorkflowEngineConfig ```