Add BioEmu Nextflow pipeline implementation

params.json

@@ -0,0 +1,106 @@
+{
+    "params": {
+        "fasta_list": {
+            "type": "file[]",
+            "description": "FASTA files containing protein sequences",
+            "default": [],
+            "required": true,
+            "pipeline_io": "input",
+            "var_name": "params.fasta_list",
+            "examples": [
+                ["/omic/olamide/examples/prot1.fasta", "/omic/olamide/examples/prot2.fasta"]
+            ],
+            "pattern": ".*\\.fasta$",
+            "validation": {},
+            "notes": "Select one or more FASTA files with protein sequences"
+        },
+        "outdir": {
+            "type": "folder",
+            "description": "Output Directory",
+            "default": "/omic/olamide/output",
+            "required": true,
+            "pipeline_io": "output",
+            "var_name": "params.outdir",
+            "examples": [
+                "/omic/olamide/output"
+            ],
+            "pattern": ".*",
+            "validation": {},
+            "notes": "Select where to save your analysis results"
+        },
+        "num_samples": {
+            "type": "integer",
+            "description": "Number of protein structure samples",
+            "default": 10,
+            "required": true,
+            "pipeline_io": "parameter",
+            "var_name": "params.num_samples",
+            "examples": [
+                "10"
+            ],
+            "pattern": "^\\d+$",
+            "validation": {
+                "min": 1
+            },
+            "notes": "More samples provide better coverage of conformational space"
+        },
+        "batch_size_100": {
+            "type": "integer",
+            "description": "Batch size parameter",
+            "default": 10,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.batch_size_100",
+            "hidden": true,
+            "examples": [
+                "10"
+            ],
+            "pattern": "^\\d+$"
+        },
+        "temperature": {
+            "type": "integer",
+            "description": "Temperature (K) for free energy",
+            "default": 300,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.temperature",
+            "examples": [
+                "300"
+            ],
+            "pattern": "^\\d+$",
+            "validation": {
+                "min": 200,
+                "max": 500
+            },
+            "notes": "Temperature in Kelvin for free energy calculations"
+        },
+        "n_clusters": {
+            "type": "integer",
+            "description": "Number of conformational clusters",
+            "default": 5,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.n_clusters",
+            "examples": [
+                "5"
+            ],
+            "pattern": "^\\d+$",
+            "validation": {
+                "min": 2
+            },
+            "notes": "Number of clusters for free energy analysis"
+        },
+        "cache_dir": {
+            "type": "folder",
+            "description": "Embeddings cache directory",
+            "default": "/tmp/bioemu_cache",
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.cache_dir",
+            "hidden": true,
+            "examples": [
+                "/tmp/bioemu_cache"
+            ]
+        }
+    }
+}