Add Nextflow pipeline for PROPKA with Docker configuration

params.json

@@ -0,0 +1,69 @@
+{
+    "params": {
+        "pdb": {
+            "type": "file",
+            "description": "Path pattern to PDB files for pKa prediction",
+            "default": "/mnt/OmicNAS/private/old/olamide/propka/input/1HPX.pdb",
+            "required": true,
+            "pipeline_io": "input",
+            "var_name": "params.pdb",
+            "examples": [
+                "/mnt/OmicNAS/private/old/olamide/propka/input/protein.pdb",
+                "/mnt/OmicNAS/private/old/olamide/propka/input/*.pdb"
+            ],
+            "pattern": ".*\\.pdb$",
+            "enum": [],
+            "validation": {},
+            "notes": "Can be a single PDB file or a pattern to match multiple PDB files."
+        },
+        "outdir": {
+            "type": "folder",
+            "description": "Directory for PROPKA prediction results",
+            "default": "/mnt/OmicNAS/private/old/olamide/propka/output",
+            "required": true,
+            "pipeline_io": "output",
+            "var_name": "params.outdir",
+            "examples": [
+                "/mnt/OmicNAS/private/old/olamide/propka/output",
+                "/path/to/custom/output"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "Directory where pKa prediction results will be stored. Will be created if it doesn't exist."
+        },
+        "ph": {
+            "type": "number",
+            "description": "pH value for titration calculations",
+            "default": 7.0,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.ph",
+            "examples": [
+                7.0,
+                5.5
+            ],
+            "validation": {
+                "min": 0.0,
+                "max": 14.0
+            },
+            "notes": "The pH value used for calculating residue protonation states."
+        },
+        "options": {
+            "type": "string",
+            "description": "Additional command-line options for PROPKA",
+            "default": "",
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.options",
+            "examples": [
+                "--titrate_only Asp,Glu",
+                "--window 1.0"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "Additional command-line options to pass to propka3. See propka3 --help for available options."
+        }
+    }
+}