Add BioEmu Nextflow pipeline implementation

nextflow.config

@@ -0,0 +1,38 @@
+// Manifest for Nextflow metadata
+manifest {
+    name = 'BioEmu-Nextflow'
+    author = 'Generated from BioEmu repository'
+    homePage = 'https://github.com/microsoft/bioemu'
+    description = 'Nextflow pipeline for BioEmu - Biomolecular Emulator for protein structure sampling'
+    mainScript = 'main.nf'
+    version = '1.0.0'
+}
+
+// Global default parameters
+params {
+    fasta = "/mnt/OmicNAS/private/old/olamide/bioemu/input/villin_headpiece.fasta"
+    outdir = "/mnt/OmicNAS/private/old/olamide/bioemu/output"
+    cache_dir = "/mnt/OmicNAS/private/old/olamide/bioemu/cache"
+    num_samples = 10
+    batch_size_100 = 10
+}
+
+// Container configurations
+docker {
+    enabled = true
+    runOptions = '--gpus all'
+}
+
+// Process configurations
+process {
+    cpus = 1
+    memory = '8 GB'
+}
+
+// Execution configurations
+executor {
+    $local {
+        cpus = 4
+        memory = '8 GB'
+    }
+}