#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow
id: inverse_fold
label: "Extra 7: Inverse fold design"
doc: |
  Catalog entry `inverse_fold` (Protocol surface, biolm-protocols
  catalog.json, protocol `biolm/inverse-fold-v1`). Structure-conditioned
  sequence design with ProteinMPNN from a backbone PDB. Runs via
  `biolm protocol run-local`.

requirements:
  InlineJavascriptRequirement: {}

inputs:
  pdb:
    type: File
    doc: "Backbone PDB file to condition sequence design on."
  batch_size:
    type: int
    default: 16
    doc: "Number of designed sequences to sample."
  temperature:
    type: float
    default: 0.1
    doc: "ProteinMPNN sampling temperature."
  protocol_file:
    type: File
    default:
      class: File
      location: ../protocols/inverse_fold/protocol.yaml
    doc: "Pinned protocol YAML. Default: in-repo protocols/<id>/protocol.yaml."
  backend:
    type: string
    default: platform
    doc: "'platform' (biolm.ai) or 'hub' (route task-model calls via hub_url)."
  hub_url:
    type: string?
    doc: "Hub gateway base URL, required when backend=hub."
  biolm_token:
    type: string?
    doc: "BIOLM_TOKEN; omit to use the ambient environment or ~/.biolm/credentials."
  demo:
    type: boolean
    default: false
    doc: "Cheap smoke-test mode: caps batch_size to at most 2."
  output_dir:
    type: string?
    doc: "Optional pipeline output directory passed through to run-local."

steps:
  build_inputs:
    run:
      class: ExpressionTool
      requirements:
        InlineJavascriptRequirement: {}
      inputs:
        pdb: File
        batch_size: int
        temperature: float
        demo: boolean
      outputs:
        inputs_json: File
      expression: |
        ${
          var payload = {
            "pdb": inputs.pdb.contents,
            "batch_size": inputs.demo ? Math.min(2, inputs.batch_size) : inputs.batch_size,
            "temperature": inputs.temperature
          };
          return {
            "inputs_json": {
              "class": "File",
              "basename": "inverse_fold.inputs.json",
              "contents": JSON.stringify(payload, null, 2)
            }
          };
        }
    in:
      pdb:
        source: pdb
        loadContents: true
      batch_size: batch_size
      temperature: temperature
      demo: demo
    out: [inputs_json]

  run_protocol:
    run: ../tools/biolm-protocol-run-local.cwl
    in:
      backend: backend
      hub_url: hub_url
      biolm_token: biolm_token
      protocol_file: protocol_file
      inputs_json: build_inputs/inputs_json
      output_dir: output_dir
    out: [result]

outputs:
  result:
    type: File
    outputSource: run_protocol/result
    doc: "JSON record with ProteinMPNN-designed sequences."