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 "${params.container_corto}"
-  containerOptions "${params.containerOptions}"
-  publishDir "${params.outdir}/${params.project_name}", mode: 'copy'
+  container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
+  publishDir params.outdir, 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)
+    predicted<-mra(TPM, 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)))
+}