Initial commit: FlowDock pipeline configured for WES execution

params.json

@@ -0,0 +1,101 @@
+{
+    "params": {
+        "input_receptor": {
+            "type": "string",
+            "description": "Protein sequence(s) in single-letter amino acid code. Multiple chains separated by '|'",
+            "default": "YNKIVHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNKLEGKVPMHKLFLEMLEAKV",
+            "required": true,
+            "pipeline_io": "input",
+            "var_name": "params.input_receptor",
+            "examples": [
+                "YNKIVHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNKLEGKVPMHKLFLEMLEAKV",
+                "MYTVKPGDTMWKIAVKYQIGISEIIAANPQIKNPNLIYPGQKINIP|MYTVKPGDTMWKIAVKYQIGISEIIAANPQIKNPNLIYPGQKINIP"
+            ],
+            "pattern": "^[ACDEFGHIKLMNPQRSTVWY|]+$",
+            "enum": [],
+            "validation": {},
+            "notes": "For multi-chain proteins, separate sequences with '|' character."
+        },
+        "input_ligand": {
+            "type": "string",
+            "description": "Ligand SMILES string for docking",
+            "default": "c1cc2c(cc1O)CCCC2",
+            "required": true,
+            "pipeline_io": "input",
+            "var_name": "params.input_ligand",
+            "examples": [
+                "c1cc2c(cc1O)CCCC2",
+                "CC(=O)NC1C(O)OC(CO)C(OC2OC(CO)C(O)C(O)C2NC(C)=O)C1O"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "SMILES notation for the ligand molecule."
+        },
+        "input_template": {
+            "type": "file",
+            "description": "Optional template PDB structure for protein. If empty, ESMFold will predict the structure",
+            "default": "",
+            "required": false,
+            "pipeline_io": "input",
+            "var_name": "params.input_template",
+            "examples": [
+                "/path/to/template.pdb",
+                ""
+            ],
+            "pattern": ".*\\.pdb$",
+            "enum": [],
+            "validation": {},
+            "notes": "Providing a template can improve docking quality. Leave empty to use ESMFold-predicted structure."
+        },
+        "sample_id": {
+            "type": "string",
+            "description": "Unique identifier for the prediction sample",
+            "default": "flowdock_sample",
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.sample_id",
+            "examples": [
+                "6i67",
+                "T1152",
+                "my_protein_ligand"
+            ],
+            "pattern": "^[a-zA-Z0-9_-]+$",
+            "enum": [],
+            "validation": {},
+            "notes": "Used for naming output directories and files."
+        },
+        "outdir": {
+            "type": "folder",
+            "description": "Directory for FlowDock output results",
+            "default": "s3://omic/eureka/flowdock/output/",
+            "required": true,
+            "pipeline_io": "output",
+            "var_name": "params.outdir",
+            "examples": [
+                "./flowdock_output",
+                "/data/predictions/flowdock"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "Directory where PDB structures and logs will be stored."
+        },
+        "n_samples": {
+            "type": "integer",
+            "description": "Number of prediction samples to generate",
+            "default": 5,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.n_samples",
+            "examples": [1, 5, 10, 40],
+            "pattern": "^[1-9][0-9]*$",
+            "enum": [],
+            "validation": {
+                "min": 1,
+                "max": 100
+            },
+            "notes": "Higher values provide more conformational diversity but increase computation time."
+        }
+    }
+}