Add LigandMPNN Nextflow pipeline for protein sequence design

nextflow.config

@@ -0,0 +1,42 @@
+// Manifest for Nextflow metadata
+manifest {
+    name = 'LigandMPNN-Nextflow'
+    author = 'Generated from LigandMPNN repository'
+    homePage = 'https://github.com/dauparas/LigandMPNN'
+    description = 'Nextflow pipeline for LigandMPNN - Protein sequence design with ligand context'
+    mainScript = 'main.nf'
+    version = '1.0.0'
+}
+
+// Global default parameters
+params {
+    pdb = "/mnt/OmicNAS/private/old/olamide/ligandmpnn/input/1BC8.pdb"
+    outdir = "/mnt/OmicNAS/private/old/olamide/ligandmpnn/output"
+    model_type = "ligand_mpnn"
+    temperature = 0.1
+    seed = 111
+    batch_size = 1
+    number_of_batches = 1
+    chains_to_design = ""
+    fixed_residues = ""
+}
+
+// Container configurations
+docker {
+    enabled = true
+    runOptions = '--gpus all'
+}
+
+// Process configurations
+process {
+    cpus = 4
+    memory = '16 GB'
+}
+
+// Execution configurations
+executor {
+    $local {
+        cpus = 8
+        memory = '32 GB'
+    }
+}