Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
}
tool: wf/secret_wf.cwl
doc: "Test secret input parameters"
}
tool: wf/secret_wf.cwl
doc: "Test secret input parameters"
+
+- job: null
+ output:
+ out: null
+ tool: wf/runin-reqs-wf.cwl
+ doc: "RunInSingleContainer handles dynamic resource requests on step"
+
+- job: null
+ output:
+ out: null
+ tool: wf/runin-reqs-wf2.cwl
+ doc: "RunInSingleContainer handles dynamic resource requests on embedded subworkflow"
+
+- job: null
+ output:
+ out: null
+ tool: wf/runin-reqs-wf3.cwl
+ should_fail: true
+ doc: "RunInSingleContainer disallows dynamic resource request on subworkflow steps"
+
+- job: null
+ output:
+ out: null
+ tool: wf/runin-reqs-wf4.cwl
+ doc: "RunInSingleContainer discovers static resource request in subworkflow steps"
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
type: int[]
default: [1, 2, 3, 4]
type: int[]
default: [1, 2, 3, 4]
+ script:
+ type: File
+ default:
+ class: File
+ location: check_mem.py
outputs:
out: []
requirements:
outputs:
out: []
requirements:
+ count: count
+ script: script
out: []
hints:
- class: arv:RunInSingleContainer
- class: ResourceRequirement
out: []
hints:
- class: arv:RunInSingleContainer
- class: ResourceRequirement
- ramMin: $(inputs.sleeptime*4)
- scatter: sleeptime
+ ramMin: $(inputs.count*4)
+ - class: arv:APIRequirement
+ scatter: count
run:
class: Workflow
id: mysub
inputs:
run:
class: Workflow
id: mysub
inputs:
+ count: int
+ script: File
outputs: []
steps:
sleep1:
in:
outputs: []
steps:
sleep1:
in:
+ count: count
+ script: script
out: []
run:
class: CommandLineTool
id: subtool
inputs:
out: []
run:
class: CommandLineTool
id: subtool
inputs:
- baseCommand: [cat, /proc/meminfo]
+ arguments: [python, $(inputs.script), $(inputs.count * 4)]
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
type: int[]
default: [1, 2, 3, 4]
type: int[]
default: [1, 2, 3, 4]
+ script:
+ type: File
+ default:
+ class: File
+ location: check_mem.py
outputs:
out: []
requirements:
outputs:
out: []
requirements:
+ count: count
+ script: script
out: []
hints:
- class: arv:RunInSingleContainer
out: []
hints:
- class: arv:RunInSingleContainer
+ - class: arv:APIRequirement
+ scatter: count
run:
class: Workflow
id: mysub
inputs:
run:
class: Workflow
id: mysub
inputs:
+ count: int
+ script: File
- - class: ResourceRequirement
- ramMin: $(inputs.sleeptime*4)
+ - class: ResourceRequirement
+ ramMin: $(inputs.count*4)
+ count: count
+ script: script
out: []
run:
class: CommandLineTool
id: subtool
inputs:
out: []
run:
class: CommandLineTool
id: subtool
inputs:
- inputBinding: {position: 1}
+ arguments: [python, $(inputs.script), $(inputs.count * 4)]
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
type: int[]
default: [1, 2, 3, 4]
type: int[]
default: [1, 2, 3, 4]
+ script:
+ type: File
+ default:
+ class: File
+ location: check_mem.py
outputs:
out: []
requirements:
outputs:
out: []
requirements:
+ count: count
+ script: script
out: []
hints:
- class: arv:RunInSingleContainer
out: []
hints:
- class: arv:RunInSingleContainer
+ - class: arv:APIRequirement
+ scatter: count
run:
class: Workflow
id: mysub
inputs:
run:
class: Workflow
id: mysub
inputs:
+ count: int
+ script: File
outputs: []
steps:
sleep1:
in:
outputs: []
steps:
sleep1:
in:
+ count: count
+ script: script
out: []
run:
class: CommandLineTool
id: subtool
hints:
- class: ResourceRequirement
out: []
run:
class: CommandLineTool
id: subtool
hints:
- class: ResourceRequirement
- ramMin: $(inputs.sleeptime*4)
+ ramMin: $(inputs.count*4)
- inputBinding: {position: 1}
+ arguments: [python, $(inputs.script), $(inputs.count * 4)]
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
type: int[]
default: [1, 2, 3, 4]
type: int[]
default: [1, 2, 3, 4]
+ script:
+ type: File
+ default:
+ class: File
+ location: check_mem.py
outputs:
out: []
requirements:
outputs:
out: []
requirements:
+ count: count
+ script: script
out: []
hints:
- class: arv:RunInSingleContainer
out: []
hints:
- class: arv:RunInSingleContainer
+ - class: arv:APIRequirement
+ scatter: count
run:
class: Workflow
id: mysub
inputs:
run:
class: Workflow
id: mysub
inputs:
+ count: int
+ script: File
outputs: []
steps:
sleep1:
in:
outputs: []
steps:
sleep1:
in:
+ count: count
+ script: script
out: []
run:
class: CommandLineTool
out: []
run:
class: CommandLineTool
- class: ResourceRequirement
ramMin: 8
inputs:
- class: ResourceRequirement
ramMin: 8
inputs:
- inputBinding: {position: 1}
+ arguments: [python, $(inputs.script), "8"]