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

 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

Slots

Name	Cardinality and Range	Description	Inheritance
cpus_per_task	0..1 xsd:integer	CPU cores requested per task (Slurm –cpus-per-task)	direct
mem	0..1 xsd:string	Memory per task in scheduler syntax (e	direct
time	0..1 xsd:string	Wall-clock limit per task (e	direct
gres	0..1 xsd:string	Generic scheduler resources, e	direct
partition	0..1 xsd:string	Scheduler partition to submit to (Slurm)	direct
account	0..1 xsd:string	Accounting allocation to charge the tasks against (Slurm)	direct
comment	0..1 xsd:string	Free-text provenance tag on each submitted job (Slurm `--comment`), visible…	direct
cores	0..1 xsd:integer	Total cores for local engines (Snakemake –cores)	direct
jobs	0..1 xsd:integer	Concurrent jobs the workflow engine keeps in flight (Snakemake `--jobs`, wr…	direct
executor	0..1 xsd:string	Executor to run the pipeline through (Nextflow process	direct
queue	0..1 xsd:string	Scheduler queue for the executor (Nextflow process	direct
modules	* xsd:string	Environment modules to load before running (module load …)	direct
venv	0..1 xsd:string	Path to a virtual environment to activate before running	direct
setup	* xsd:string	Shell lines run verbatim before the task command, after `set -euo pipefail`…	direct
mail_type	0..1 xsd:string	Scheduler notification trigger (e	direct
mail_user	0..1 xsd:string	Notification email address	direct
array_chunk	0..1 xsd:integer	Overrides ``distribute	direct
options	* SchedulerDirective	Additional engine-native scheduler directives passed through verbatim, each i…	direct
env	* EnvironmentVariable	Environment variables exported before the task command on every engine (e	direct

Usages

used by	used in	type	used
WorkflowConfig	slurm	range	WorkflowEngineConfig
WorkflowConfig	snakemake	range	WorkflowEngineConfig
WorkflowConfig	nextflow	range	WorkflowEngineConfig

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

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:<study>/exp_<experiment>``
      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
      <name>``), 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 --<name>=<value>`` line,
      a Snakemake ``resources:`` entry, or a Nextflow ``process.<name>`` 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

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:<study>/exp_<experiment>``
      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
      <name>``), 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 --<name>=<value>`` line,
      a Snakemake ``resources:`` entry, or a Nextflow ``process.<name>`` 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