Configure corto for WES k8s execution

- Update main.nf: hardcode Harbor container image, add workflow block,
  use PVC mount path defaults, remove stageInMode copy and legacy params
- Update nextflow.config: add k8s profile with container, add process
  resource limits, update manifest to point to Gitea
- Update params.json: use s3:// prefixed paths for WES, remove
  container_corto, containerOptions, and project_name params

main.nf

@@ -1,19 +1,21 @@
+#!/usr/bin/env nextflow
+
 nextflow.enable.dsl=2
 
+// Parameters
+params.TPM = '/omic/eureka/corto/20002_1289_female_patient_0_TPM.csv'
+params.regulon = '/omic/eureka/corto/regulon.rda'
+params.outdir = '/omic/eureka/corto/output'
+
 process CORTO {
-  container "${params.container_corto}"
+  container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
-  containerOptions "${params.containerOptions}"
+  publishDir params.outdir, mode: 'copy'
-  publishDir "${params.outdir}/${params.project_name}", mode: 'copy'
   debug true
-  // maxForks 1
-  stageInMode 'copy'
 
   input:
     path TPM
     path regulon
-    // path TPM_ref
 
-  // Define output channels
   output:
     path "*_metabolome.csv", emit: csv_metabol
 
@@ -24,21 +26,17 @@ process CORTO {
     library(data.table)
 
     TPM <- as.matrix(fread("$TPM"),rownames=1)
-    #TPM_ref <- as.matrix(fread("TPM_ref"),rownames=1) #dollar sign is missing
-
-    #try normalization; dont use
-    #TPM <- scale(TPM)
-    #TPM_log2 = log2(TPM + 1)
 
     load("$regulon")
 
     predicted<-mra(TPM, regulon=regulon)
 
-    #use this if we want to compare patients and reference TPM, data formet output is not csv -> work on data saving if needed
-    #predicted<-mra(TPM, path TPM_ref, regulon=regulon)
-
     name = strsplit(strsplit("$TPM", split = "/")[[1]][length(strsplit("$TPM", split = "/")[[1]])],  split = "_TPM.csv")[[1]][1]
     name = paste(name, "_metabolome.csv", sep="")
     write.csv(predicted, name)
     """
 }
+
+workflow {
+  CORTO(Channel.of(file(params.TPM)), Channel.of(file(params.regulon)))
+}

nextflow.config

@@ -1,15 +1,34 @@
 manifest {
-    name                = 'corto'
+    name            = 'corto'
-    author              = 'omic'
+    author          = 'omic'
-    recurseSubmodules   = true
+    homePage        = 'https://trs-gitea.cluster.omic.ai/omic/corto'
-    homePage            = 'https://gitlab.com/omic/next/registry/tools/corto'
+    description     = 'CORTO - Correlation Tool for gene regulatory network analysis'
-    description         = ''
+    mainScript      = 'main.nf'
-    mainScript          = 'main.nf'
+    version         = '1.0.0'
-    nextflowVersion     = '!>=21.04.3'
+    defaultBranch   = 'master'
-    defaultBranch       = 'master'
 }
 
-docker {
+params {
-    enabled = true
+    TPM = null
-    temp = 'auto'
+    regulon = null
+    outdir = null
+}
+
+profiles {
+    standard {
+        docker {
+            enabled = true
+            temp = 'auto'
+        }
+    }
+    k8s {
+        process {
+            container = 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
+        }
+    }
+}
+
+process {
+    cpus = 1
+    memory = '4 GB'
 }

params.json

@@ -3,13 +3,12 @@
         "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",
+            "default": "s3://omic/eureka/corto/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",
+                "s3://omic/eureka/corto/20002_1289_female_patient_0_TPM.csv"
-                "/path/to/your/sample_TPM.csv"
             ],
             "pattern": ".*\\.csv$",
             "enum": [],
@@ -19,13 +18,12 @@
         "regulon": {
             "type": "file",
             "description": "Path to regulon RDA file",
-            "default": "/data/olamide/corto/corto_metabolite_prediction/regulon.rda",
+            "default": "s3://omic/eureka/corto/regulon.rda",
             "required": true,
             "pipeline_io": "input",
             "var_name": "params.regulon",
             "examples": [
-                "/data/olamide/corto/corto_metabolite_prediction/regulon.rda",
+                "s3://omic/eureka/corto/regulon.rda"
-                "/path/to/your/custom_regulon.rda"
             ],
             "pattern": ".*\\.rda$",
             "enum": [],
@@ -35,67 +33,17 @@
         "outdir": {
             "type": "folder",
             "description": "Directory for CORTO analysis results",
-            "default": "/mnt/OmicNAS/private/old/gabe/corto/outputs",
+            "default": "s3://omic/eureka/corto/output",
             "required": true,
             "pipeline_io": "output",
             "var_name": "params.outdir",
             "examples": [
-                "/mnt/OmicNAS/private/old/gabe/corto/outputs",
+                "s3://omic/eureka/corto/output"
-                "/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"
         }
     }
 }