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

nextflow.config

@@ -1,15 +1,34 @@
 manifest {
-    name                = 'corto'
-    author              = 'omic'
-    recurseSubmodules   = true
-    homePage            = 'https://gitlab.com/omic/next/registry/tools/corto'
-    description         = ''
-    mainScript          = 'main.nf'
-    nextflowVersion     = '!>=21.04.3'
-    defaultBranch       = 'master'
+    name            = 'corto'
+    author          = 'omic'
+    homePage        = 'https://trs-gitea.cluster.omic.ai/omic/corto'
+    description     = 'CORTO - Correlation Tool for gene regulatory network analysis'
+    mainScript      = 'main.nf'
+    version         = '1.0.0'
+    defaultBranch   = 'master'
 }
 
-docker {
-    enabled = true
-    temp = 'auto'
+params {
+    TPM = null
+    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'
 }