Configure foldseek pipeline for WES execution

- Update container image to harbor.cluster.omic.ai/omic/foldseek:latest
- Update default paths to /omic/eureka/foldseek/ PVC mount paths
- Add k8s profile with eureka-pvc storage
- Remove stageInMode copy and containerOptions for k8s compatibility
- Update params.json defaults to s3://omic/eureka/foldseek/ paths

main.nf

@@ -2,9 +2,9 @@
 
 nextflow.enable.dsl=2
 
-params.query = '/mnt/OmicNAS/private/old/olamide/foldseek/input/1CRN.pdb'
-params.target = '/mnt/OmicNAS/private/old/olamide/foldseek/input/'
-params.outdir = '/mnt/OmicNAS/private/old/olamide/foldseek/output/'
+params.query = '/omic/eureka/foldseek/input/1CRN.pdb'
+params.target = '/omic/eureka/foldseek/input/'
+params.outdir = '/omic/eureka/foldseek/output'
 params.mode = 'search'
 params.sensitivity = 9.5
 params.evalue = 0.001
@@ -14,10 +14,8 @@ params.coverage = 0.0
 params.format_output = 'query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits'
 
 process FOLDSEEK_SEARCH {
-    container 'foldseek:latest'
-    containerOptions '-v /mnt:/mnt'
+    container 'harbor.cluster.omic.ai/omic/foldseek:latest'
     publishDir params.outdir, mode: 'copy'
-    stageInMode 'copy'
 
     input:
         path query
@@ -47,10 +45,8 @@ process FOLDSEEK_SEARCH {
 }
 
 process FOLDSEEK_CLUSTER {
-    container 'foldseek:latest'
-    containerOptions '-v /mnt:/mnt'
+    container 'harbor.cluster.omic.ai/omic/foldseek:latest'
     publishDir params.outdir, mode: 'copy'
-    stageInMode 'copy'
 
     input:
         path structures
@@ -77,10 +73,8 @@ process FOLDSEEK_CLUSTER {
         """
 }
 process FOLDSEEK_MULTIMER_SEARCH {
-    container 'foldseek:latest'
-    containerOptions '-v /mnt:/mnt'
+    container 'harbor.cluster.omic.ai/omic/foldseek:latest'
     publishDir params.outdir, mode: 'copy'
-    stageInMode 'copy'
 
     input:
         path query
@@ -107,10 +101,8 @@ process FOLDSEEK_MULTIMER_SEARCH {
 }
 
 process FOLDSEEK_CREATEDB {
-    container 'foldseek:latest'
-    containerOptions '-v /mnt:/mnt'
+    container 'harbor.cluster.omic.ai/omic/foldseek:latest'
     publishDir params.outdir, mode: 'copy'
-    stageInMode 'copy'
 
     input:
         path structures