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

nextflow.config

@@ -1,18 +1,15 @@
-// Manifest for Nextflow metadata
 manifest {
-    name = 'Foldseek-Nextflow'
-    author = 'Generated from Foldseek repository'
-    homePage = 'https://github.com/steineggerlab/foldseek'
+    name = 'foldseek'
+    author = 'Olamide'
     description = 'Nextflow pipeline for Foldseek - Fast protein structure search and clustering'
     mainScript = 'main.nf'
     version = '1.0.0'
 }
 
-// Global default parameters
 params {
-    query = "/mnt/OmicNAS/private/old/olamide/foldseek/input/1CRN.pdb"
-    target = "/mnt/OmicNAS/private/old/olamide/foldseek/input/"
-    outdir = "/mnt/OmicNAS/private/old/olamide/foldseek/output"
+    query = "/omic/eureka/foldseek/input/1CRN.pdb"
+    target = "/omic/eureka/foldseek/input/"
+    outdir = "/omic/eureka/foldseek/output"
     mode = "search"
     sensitivity = 9.5
     evalue = 0.001
@@ -22,22 +19,30 @@ params {
     format_output = "query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits"
 }
 
-// Container configurations
 docker {
     enabled = true
-    runOptions = '-v /mnt:/mnt'
 }
 
-// Process configurations
 process {
+    container = 'harbor.cluster.omic.ai/omic/foldseek:latest'
     cpus = 4
     memory = '16 GB'
 }
 
-// Execution configurations
-executor {
-    $local {
-        cpus = 8
-        memory = '32 GB'
+profiles {
+    standard {
+        docker {
+            temp = 'auto'
+        }
+    }
+
+    k8s {
+        process {
+            executor = 'k8s'
+        }
+        k8s {
+            storageClaimName = 'eureka-pvc'
+            storageMountPath = '/omic/eureka'
+        }
     }
 }