Update CORTO pipeline with params.json and workflow improvements

params.json

@@ -0,0 +1,101 @@
+{
+    "params": {
+        "TPM": {
+            "type": "file",
+            "description": "Path to TPM (Transcripts Per Million) CSV file",
+            "default": "/data/olamide/corto/corto_metabolite_prediction/20002_1289_female_patient_0_TPM.csv",
+            "required": true,
+            "pipeline_io": "input",
+            "var_name": "params.TPM",
+            "examples": [
+                "/data/olamide/corto/corto_metabolite_prediction/20002_1289_female_patient_0_TPM.csv",
+                "/path/to/your/sample_TPM.csv"
+            ],
+            "pattern": ".*\\.csv$",
+            "enum": [],
+            "validation": {},
+            "notes": "A CSV file containing TPM values with ENSG IDs as rows and samples as columns"
+        },
+        "regulon": {
+            "type": "file",
+            "description": "Path to regulon RDA file",
+            "default": "/data/olamide/corto/corto_metabolite_prediction/regulon.rda",
+            "required": true,
+            "pipeline_io": "input",
+            "var_name": "params.regulon",
+            "examples": [
+                "/data/olamide/corto/corto_metabolite_prediction/regulon.rda",
+                "/path/to/your/custom_regulon.rda"
+            ],
+            "pattern": ".*\\.rda$",
+            "enum": [],
+            "validation": {},
+            "notes": "An R data file containing regulon information for the CORTO analysis"
+        },
+        "outdir": {
+            "type": "folder",
+            "description": "Directory for CORTO analysis results",
+            "default": "/mnt/OmicNAS/private/old/gabe/corto/outputs",
+            "required": true,
+            "pipeline_io": "output",
+            "var_name": "params.outdir",
+            "examples": [
+                "/mnt/OmicNAS/private/old/gabe/corto/outputs",
+                "/path/to/custom/output"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "Directory where metabolome prediction results will be stored"
+        },
+        "project_name": {
+            "type": "string",
+            "description": "Project name for output directory organization",
+            "default": "test",
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.project_name",
+            "examples": [
+                "test",
+                "patient_analysis",
+                "metabolite_prediction_run1"
+            ],
+            "pattern": "^[A-Za-z0-9_-]+$",
+            "enum": [],
+            "validation": {},
+            "notes": "Name used to create a subdirectory within the output directory"
+        },
+        "container_corto": {
+            "type": "string",
+            "description": "Docker container for CORTO",
+            "default": "corto:latest",
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.container_corto",
+            "examples": [
+                "corto:latest",
+                "yourregistry/corto:v1.0"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "Docker container image to use for the CORTO analysis"
+        },
+        "containerOptions": {
+            "type": "string",
+            "description": "Docker container options",
+            "default": "--gpus all --rm -v /mnt:/mnt",
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.containerOptions",
+            "examples": [
+                "--gpus all --rm -v /mnt:/mnt",
+                "--rm -v /custom/path:/mnt"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "Options to pass to the Docker container runtime"
+        }
+    }
+}