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_vcf2prot.nf

@@ -7,7 +7,6 @@ process VCF2PROT {
   containerOptions "${params.containerOptions}"
   // echo true
   publishDir "${params.outdir}/vcf2prot", mode: 'copy'
-  stageInMode 'copy'
   maxForks 1
 
   input: