Configure pipeline for WES execution with Harbor image and s3 paths

main.nf

@@ -2,8 +2,8 @@
 
 nextflow.enable.dsl=2
 
-params.pdb = '/mnt/OmicNAS/private/old/olamide/ligandmpnn/input/1BC8.pdb'
+params.pdb = 's3://omic/eureka/ligandmpnn/1BC8'
-params.outdir = '/mnt/OmicNAS/private/old/olamide/ligandmpnn/output'
+params.outdir = 's3://omic/eureka/ligandmpnn/output'
 params.model_type = 'ligand_mpnn'
 params.temperature = 0.1
 params.seed = 111
@@ -14,8 +14,7 @@ params.fixed_residues = ''
 params.pack_side_chains = 0
 
 process LIGANDMPNN {
-    container 'ligandmpnn:latest'
+    container 'harbor.cluster.omic.ai/omic/ligandmpnn:latest'
-    containerOptions '--rm --gpus all -v /mnt:/mnt'
     publishDir params.outdir, mode: 'copy'
     stageInMode 'copy'
 

nextflow.config

@@ -10,8 +10,8 @@ manifest {
 
 // Global default parameters
 params {
-    pdb = "/mnt/OmicNAS/private/old/olamide/ligandmpnn/input/1BC8.pdb"
+    pdb = "s3://omic/eureka/ligandmpnn/1BC8"
-    outdir = "/mnt/OmicNAS/private/old/olamide/ligandmpnn/output"
+    outdir = "s3://omic/eureka/ligandmpnn/output"
     model_type = "ligand_mpnn"
     temperature = 0.1
     seed = 111
@@ -40,3 +40,15 @@ executor {
         memory = '32 GB'
     }
 }
+
+// Kubernetes profile for WES execution
+profiles {
+    k8s {
+        docker.enabled = false
+        process.container = 'harbor.cluster.omic.ai/omic/ligandmpnn:latest'
+    }
+    k8s_gpu {
+        docker.enabled = false
+        process.container = 'harbor.cluster.omic.ai/omic/ligandmpnn:latest'
+    }
+}