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134 changes: 134 additions & 0 deletions
134
src/blue_cwl/generators/memodel/neurons_memodel/v3/definition.cwl
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Original file line number | Diff line number | Diff line change |
---|---|---|
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cwlVersion: v1.2 | ||
class: Workflow | ||
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id: workflow_me_model | ||
label: workflow-me-model | ||
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inputs: | ||
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- id: configuration_id | ||
type: NexusType | ||
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- id: circuit_id | ||
type: NexusType | ||
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- id: output_dir | ||
type: Directory | ||
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outputs: | ||
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- id: circuit | ||
type: NexusType | ||
outputSource: register/circuit | ||
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steps: | ||
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- id: setup | ||
in: | ||
output_dir: output_dir | ||
out: | ||
- stage_dir | ||
- build_dir | ||
run: ./setup.cwl | ||
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- id: stage | ||
in: | ||
stage_dir: setup/stage_dir | ||
circuit_id: circuit_id | ||
configuration_id: configuration_id | ||
out: | ||
- config_file | ||
- circuit_file | ||
- nodes_file | ||
- morphologies_dir | ||
run: ./stage.cwl | ||
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- id: recipe | ||
run: ./recipe.cwl | ||
in: | ||
config_file: stage/config_file | ||
output_file: | ||
source: setup/build_dir | ||
valueFrom: $(self.path)/recipe.json | ||
out: | ||
- recipe_file | ||
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- id: emodel_prepare | ||
run: ./emodel_prepare.cwl | ||
in: | ||
config_file: recipe/recipe_file | ||
work_dir: | ||
source: setup/build_dir | ||
valueFrom: $(self.path)/configs | ||
out_mechanisms_dir: | ||
source: setup/build_dir | ||
valueFrom: $(self.path)/mechanisms | ||
out: | ||
- work_dir | ||
- mechanisms_dir | ||
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- id: emodel_assign | ||
run: ./emodel_assign.cwl | ||
in: | ||
nodes_file: stage/nodes_file | ||
recipe_file: recipe/recipe_file | ||
out_nodes_file: | ||
source: setup/build_dir | ||
valueFrom: $(self.path)/assign_nodes.h5 | ||
out_configs_dir: | ||
source: setup/build_dir | ||
valueFrom: $(self.path)/configs | ||
out: | ||
- nodes_file | ||
- configs_dir | ||
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- id: emodel_adapt | ||
run: ./emodel_adapt.cwl | ||
in: | ||
nodes_file: emodel_assign/nodes_file | ||
recipe_file: recipe/recipe_file | ||
configs_dir: emodel_assign/configs_dir | ||
mechanisms_dir: emodel_prepare/mechanisms_dir | ||
morphologies_dir: stage/morphologies_dir | ||
work_dir: | ||
source: setup/build_dir | ||
valueFrom: $(self.path)/adapt_workdir | ||
out_nodes_file: | ||
source: setup/build_dir | ||
valueFrom: $(self.path)/adapt_nodes.h5 | ||
out_hoc_dir: | ||
source: setup/build_dir | ||
valueFrom: $(self.path)/hoc | ||
parallel_lib: | ||
valueFrom: multiprocessing | ||
out: | ||
- hoc_dir | ||
- nodes_file | ||
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- id: emodel_currents | ||
run: ./emodel_currents.cwl | ||
in: | ||
hoc_dir: emodel_adapt/hoc_dir | ||
recipe_file: recipe/recipe_file | ||
circuit_file: stage/circuit_file | ||
nodes_file: emodel_adapt/nodes_file | ||
morphologies_dir: stage/morphologies_dir | ||
mechanisms_dir: emodel_prepare/mechanisms_dir | ||
out_nodes_file: | ||
source: setup/build_dir | ||
valueFrom: $(self.path)/nodes.h5 | ||
parallel_lib: | ||
valueFrom: multiprocessing | ||
out: | ||
- nodes_file | ||
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- id: register | ||
run: ./register.cwl | ||
in: | ||
circuit_id: circuit_id | ||
circuit_file: stage/circuit_file | ||
hoc_dir: emodel_adapt/hoc_dir | ||
nodes_file: emodel_currents/nodes_file | ||
output_dir: output_dir | ||
out: | ||
- circuit |
87 changes: 87 additions & 0 deletions
87
src/blue_cwl/generators/memodel/neurons_memodel/v3/emodel_adapt.cwl
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Original file line number | Diff line number | Diff line change |
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cwlVersion: v1.2 | ||
class: CommandLineTool | ||
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id: emodel_adapt | ||
label: emodel-adapt | ||
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environment: | ||
env_type: MODULE | ||
modules: | ||
- unstable | ||
- py-emodel-generalisation | ||
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executor: | ||
type: slurm | ||
slurm_config: | ||
partition: prod | ||
account: proj134 | ||
exclusive: true | ||
time: '11:00:00' | ||
constraint: nvme | ||
nodes: 1 | ||
mem: 0 | ||
remote_config: | ||
host: bbpv1.epfl.ch | ||
env_vars: | ||
NEURON_MODULE_OPTIONS: --nogui | ||
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baseCommand: ["emodel-generalisation", "-v", "--no-progress", "adapt", "--no-reuse"] | ||
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inputs: | ||
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- id: nodes_file | ||
type: File | ||
inputBinding: | ||
prefix: --input-node-path | ||
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- id: out_nodes_file | ||
type: string | ||
inputBinding: | ||
prefix: --output-node-path | ||
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- id: morphologies_dir | ||
type: Directory | ||
inputBinding: | ||
prefix: --morphology-path | ||
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- id: mechanisms_dir | ||
type: Directory | ||
inputBinding: | ||
prefix: --mech-path | ||
|
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- id: recipe_file | ||
type: File | ||
inputBinding: | ||
prefix: --config-path | ||
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- id: out_hoc_dir | ||
type: string | ||
inputBinding: | ||
prefix: --output-hoc-path | ||
|
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- id: configs_dir | ||
type: Directory | ||
inputBinding: | ||
prefix: --local-config-path | ||
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- id: work_dir | ||
type: string | ||
inputBinding: | ||
prefix: --local-dir | ||
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- id: parallel_lib | ||
type: string | ||
inputBinding: | ||
prefix: --parallel-lib | ||
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outputs: | ||
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- id: nodes_file | ||
type: File | ||
outputBinding: | ||
glob: $(inputs.out_nodes_file) | ||
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- id: hoc_dir | ||
type: Directory | ||
outputBinding: | ||
glob: $(inputs.out_hoc_dir) |
61 changes: 61 additions & 0 deletions
61
src/blue_cwl/generators/memodel/neurons_memodel/v3/emodel_assign.cwl
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,61 @@ | ||
cwlVersion: v1.2 | ||
class: CommandLineTool | ||
|
||
id: emodel_assign | ||
label: emodel-assign | ||
|
||
environment: | ||
env_type: MODULE | ||
modules: | ||
- unstable | ||
- py-emodel-generalisation | ||
|
||
executor: | ||
type: slurm | ||
slurm_config: | ||
partition: prod | ||
account: proj134 | ||
exclusive: true | ||
time: '01:00:00' | ||
nodes: 1 | ||
mem: 0 | ||
remote_config: | ||
host: bbpv1.epfl.ch | ||
env_vars: | ||
NEURON_MODULE_OPTIONS: --nogui | ||
|
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baseCommand: ["emodel-generalisation", "-v", "--no-progress", "assign"] | ||
|
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inputs: | ||
|
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- id: nodes_file | ||
type: File | ||
inputBinding: | ||
prefix: --input-node-path | ||
|
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- id: recipe_file | ||
type: File | ||
inputBinding: | ||
prefix: --config-path | ||
|
||
- id: out_nodes_file | ||
type: string | ||
inputBinding: | ||
prefix: --output-node-path | ||
|
||
- id: out_configs_dir | ||
type: string | ||
inputBinding: | ||
prefix: --local-config-path | ||
|
||
outputs: | ||
|
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- id: nodes_file | ||
type: File | ||
outputBinding: | ||
glob: $(inputs.out_nodes_file) | ||
|
||
- id: configs_dir | ||
type: Directory | ||
outputBinding: | ||
glob: $(inputs.out_configs_dir) |
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