Configure pipeline for WES execution on k8s cluster

- Add main.nf as WES entry point with PVC-based paths
- Update nextflow.config with k8s/k8s_gpu profiles (eureka-pvc)
- Update params.json defaults to /omic/eureka/digital-patients/ paths
- Remove stageInMode 'copy' from corto and vcf2prot for k8s compat
- Add reassemble.nf for one-time chunk reassembly on PVC

main_corto.nf

@@ -8,7 +8,6 @@ process CORTO {
   publishDir "${params.outdir}/${params.project_name}", mode: 'copy'
   // debug true
   // maxForks 1
-  stageInMode 'copy'
 
   input:
     path TPM