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.outdir = '/mnt/OmicNAS/private/old/olamide/ligandmpnn/output'
+params.pdb = 's3://omic/eureka/ligandmpnn/1BC8'
+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'
-    containerOptions '--rm --gpus all -v /mnt:/mnt'
+    container 'harbor.cluster.omic.ai/omic/ligandmpnn:latest'
     publishDir params.outdir, mode: 'copy'
     stageInMode 'copy'