Add WES pipeline configuration for pocketminer

- Add Nextflow pipeline (main.nf) with Harbor container image
- Add nextflow.config with k8s/k8s_gpu/standard profiles
- Add params.json for TRS/WES parameter discovery
- Add Dockerfile, entrypoint.py, meta.yml from original implementation
- Update paths to use /omic/eureka/Pocketminer/ convention
- Update .gitignore to allow params.json

main.nf

@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+// Parameters
+params.pdb = '/omic/eureka/Pocketminer/1HSG.pdb'
+params.outdir = '/omic/eureka/Pocketminer/output'
+params.model_path = '/workspace/gvp/models/pocketminer'
+params.debug = false
+
+// Process definition
+process POCKETMINER {
+    container 'harbor.cluster.omic.ai/omic/pocketminer:latest'
+    publishDir params.outdir, mode: 'copy'
+    stageInMode 'copy'
+
+    input:
+    path pdb_file
+
+    output:
+    path "*-preds.npy", emit: predictions_npy
+    path "*-predictions.txt", emit: predictions_txt
+    path "*-summary.json", emit: summary
+    path "*_X.npy", optional: true, emit: features_debug
+    path "*_S.npy", optional: true, emit: sequence_debug
+    path "*_mask.npy", optional: true, emit: mask_debug
+
+    script:
+    def pdb_basename = pdb_file.baseName
+    def debug_flag = params.debug ? '--debug' : ''
+    """
+    python /workspace/entrypoint.py \\
+        --pdb ${pdb_file} \\
+        --output-folder . \\
+        --output-name ${pdb_basename} \\
+        --model-path ${params.model_path} \\
+        ${debug_flag}
+    """
+}
+
+// Workflow
+workflow {
+    POCKETMINER(Channel.of(file(params.pdb)))
+}