Configure ImmuneBuilder pipeline for WES execution

- Update container image to harbor.cluster.omic.ai/omic/immunebuilder:latest
- Update input/output paths to S3 (s3://omic/eureka/immunebuilder/)
- Remove local mount containerOptions (not needed in k8s)
- Update homepage to Gitea repo URL
- Clean history to remove large model weight blobs

nextflow.config

@@ -0,0 +1,105 @@
+// Manifest for Nextflow metadata
+manifest {
+    name = 'ImmuneBuilder-Nextflow'
+    author = 'Olamide'
+    homePage = 'https://trs-gitea.cluster.omic.ai/omic/immunebuilder'
+    description = 'Nextflow pipeline for ImmuneBuilder - Deep-Learning models for predicting structures of immune proteins (antibodies, nanobodies, TCRs)'
+    mainScript = 'main.nf'
+    version = '1.2.0'
+}
+
+// Global default parameters
+params {
+    fasta = "s3://omic/eureka/immunebuilder/antibody_test.fasta"
+    outdir = "s3://omic/eureka/immunebuilder/output"
+    mode = 'antibody'
+    verbose = true
+    original_weights = false
+}
+
+// Container configurations
+docker {
+    enabled = true
+    runOptions = '-u $(id -u):$(id -g)'
+}
+
+// Process configurations
+process {
+    cpus = 4
+    memory = '16 GB'
+    time = '2h'
+
+    withName: 'ABODYBUILDER2' {
+        cpus = 4
+        memory = '16 GB'
+    }
+
+    withName: 'NANOBODYBUILDER2' {
+        cpus = 4
+        memory = '16 GB'
+    }
+
+    withName: 'TCRBUILDER2' {
+        cpus = 4
+        memory = '16 GB'
+    }
+}
+
+// Executor configurations
+executor {
+    $local {
+        cpus = 8
+        memory = '32 GB'
+    }
+}
+
+// Profile configurations
+profiles {
+    standard {
+        docker.enabled = true
+    }
+
+    gpu {
+        docker.enabled = true
+        docker.runOptions = '-u $(id -u):$(id -g) --gpus all'
+        process {
+            containerOptions = '--rm --gpus all -v /mnt:/mnt'
+        }
+    }
+
+    singularity {
+        singularity.enabled = true
+        singularity.autoMounts = true
+        docker.enabled = false
+    }
+
+    conda {
+        conda.enabled = true
+        docker.enabled = false
+    }
+}
+
+// Logging and reporting
+timeline {
+    enabled = true
+    file = "${params.outdir}/pipeline_info/timeline.html"
+    overwrite = true
+}
+
+report {
+    enabled = true
+    file = "${params.outdir}/pipeline_info/report.html"
+    overwrite = true
+}
+
+trace {
+    enabled = true
+    file = "${params.outdir}/pipeline_info/trace.txt"
+    overwrite = true
+}
+
+dag {
+    enabled = true
+    file = "${params.outdir}/pipeline_info/dag.html"
+    overwrite = true
+}