@prefix CommandLineBinding: .
@prefix EnvVarRequirement: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix SoftwarePackage: .
@prefix ns1: .
@prefix SoftwareRequirement: .
@prefix rdf: .
@prefix EnvironmentDef: .
@prefix cwl: .
@prefix ExpressionTool: .
cwl:source .
cwl:source .
rdfs:comment "Cheap smoke-test mode: caps batch_size to at most 2." ;
sld:default false ;
sld:type xsd:boolean .
rdfs:comment "Number of designed sequences to sample." ;
sld:default 16 ;
sld:type xsd:int .
cwl:loadContents true ;
cwl:source .
rdfs:comment "Backbone PDB file to condition sequence design on." ;
sld:type cwl:File .
sld:type cwl:File .
a cwl:File .
cwl:source .
rdfs:comment "JSON object of protocol input name -> value." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--inputs" ] ;
sld:type cwl:File .
rdfs:comment "ProteinMPNN sampling temperature." ;
sld:default 1e-01 ;
sld:type xsd:float .
cwl:source .
rdfs:comment "Path to a Local Protocol Profile YAML (pinned from biolm-protocols)." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--protocol" ] ;
sld:type cwl:File .
rdfs:comment "Hub gateway base URL, required when backend=hub." ;
sld:type xsd:string , sld:null .
a cwl:Workflow ;
rdfs:comment "Catalog entry `inverse_fold` (Protocol surface, biolm-protocols\ncatalog.json, protocol `biolm/inverse-fold-v1`). Structure-conditioned\nsequence design with ProteinMPNN from a backbone PDB. Runs via\n`biolm protocol run-local`.\n" ;
rdfs:label "Extra 7: Inverse fold design" ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:type xsd:int .
cwl:source .
rdfs:comment "'platform' (biolm.ai) or 'hub' (route task-model calls via hub_url)." ;
sld:default "platform" ;
sld:type xsd:string .
cwl:in , , , ;
cwl:out ;
cwl:run [ a cwl:ExpressionTool ;
ExpressionTool:expression "${\n var payload = {\n \"pdb\": inputs.pdb.contents,\n \"batch_size\": inputs.demo ? Math.min(2, inputs.batch_size) : inputs.batch_size,\n \"temperature\": inputs.temperature\n };\n return {\n \"inputs_json\": {\n \"class\": \"File\",\n \"basename\": \"inverse_fold.inputs.json\",\n \"contents\": JSON.stringify(payload, null, 2)\n }\n };\n}\n" ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ]
] .
sld:type xsd:boolean .
rdfs:comment "Pinned protocol YAML. Default: in-repo protocols//protocol.yaml." ;
sld:default ;
sld:type cwl:File .
rdfs:comment "'platform' (default biolm.ai API) or 'hub' (route task-model calls via hub_url)." ;
sld:default "platform" ;
sld:type xsd:string .
rdfs:comment "JSON record with ProteinMPNN-designed sequences." ;
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "BIOLM_TOKEN; omit to use the ambient environment or ~/.biolm/credentials." ;
sld:type xsd:string , sld:null .
cwl:source .
rdfs:comment "Hub gateway base URL (e.g. http://127.0.0.1:8000). Required when backend=hub." ;
sld:type xsd:string , sld:null .
cwl:in , , , , , ;
cwl:out ;
cwl:run .
rdfs:comment "Optional pipeline output directory." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--output-dir" ] ;
sld:type xsd:string , sld:null .
sld:type cwl:File .
cwl:source .
rdfs:comment "BIOLM_TOKEN value. Omit to use BIOLM_TOKEN already in the environment or ~/.biolm/credentials." ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
rdfs:comment "JSON records produced by the local protocol run." ;
cwl:outputBinding [ CommandOutputBinding:glob
"result.json" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:comment "Wraps `biolm protocol run-local --input k=v ...` from\nbiolm-sdk (requires `pip install \"biolm-sdk[pipeline]\"`). Task model calls\nmade by the protocol honor the platform|hub backend switch, which is why\n`run-local` (not hosted `biolm protocol run`) is the default execution\nsurface for protocol-backed workflows in this repo.\n\nCWL callers supply protocol inputs as one JSON object (`inputs_json`)\ninstead of hand-building repeated --input flags; a small driver script\nexpands that object into `--input key=` pairs and shells out\nto the real `biolm` CLI.\n" ;
rdfs:label "BioLM protocol run-local (CLI)" ;
ns1:original_cwlVersion "v1.2" ;
cwl:baseCommand ( "python3" "run_protocol_local.py" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "biolm-sdk" ;
SoftwarePackage:specs
]
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biolm-cwl:latest"
] ;
cwl:inputs , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "import argparse\nimport json\nimport subprocess\nimport sys\nfrom pathlib import Path\n\nparser = argparse.ArgumentParser()\nparser.add_argument(\"--protocol\", required=True)\nparser.add_argument(\"--inputs\", required=True)\nparser.add_argument(\"--output-dir\", default=None)\nargs = parser.parse_args()\n\npayload = json.loads(Path(args.inputs).read_text())\nif not isinstance(payload, dict):\n sys.exit(\"--inputs JSON must be an object mapping protocol input names to values\")\n\ncmd = [\"biolm\", \"protocol\", \"run-local\", args.protocol]\nfor key, value in payload.items():\n cmd += [\"--input\", \"{}={}\".format(key, json.dumps(value))]\ncmd.append(\"--json\")\nif args.output_dir:\n cmd += [\"--output-dir\", args.output_dir]\n\nproc = subprocess.run(cmd, capture_output=True, text=True)\nsys.stderr.write(proc.stderr)\nif proc.returncode != 0:\n sys.stderr.write(proc.stdout)\n sys.exit(proc.returncode)\n\nPath(\"result.json\").write_text(proc.stdout)\nsys.stdout.write(proc.stdout)\n" ;
cwl:entryname "run_protocol_local.py"
]
] ;
cwl:requirements [ a cwl:EnvVarRequirement ;
EnvVarRequirement:envDef [ EnvironmentDef:envName "BIOLM_TOKEN" ;
EnvironmentDef:envValue "$(inputs.biolm_token ? inputs.biolm_token : \"\")"
] ;
EnvVarRequirement:envDef [ EnvironmentDef:envName "BIOLM_BASE_API_URL" ;
EnvironmentDef:envValue "$(inputs.backend == \"hub\" && inputs.hub_url ? inputs.hub_url : \"\")"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
rdfs:comment "Optional pipeline output directory passed through to run-local." ;
sld:type xsd:string , sld:null .
sld:type xsd:float .