Fix ConcurrentModificationException and configuration warnings

This commit resolves three critical issues:

1. ConcurrentModificationException in protein_design.nf (line 240)
   - Replaced meta.clone() with explicit map creation to avoid concurrent
     modification issues when processing channels in parallel
   - This was causing pipeline execution to fail completely

2. Undefined parameter warnings for num_designs and budget
   - Added parameter initialization with null values in nextflow.config
   - These parameters are typically set per-sample in the samplesheet

3. Deprecated docker.userEmulation configuration warning
   - Removed deprecated docker.userEmulation setting from nextflow.config
   - The functionality is already provided by docker.runOptions

All warnings have been eliminated and the pipeline should now execute without errors.

Author: Seqera AI

FIXES_SUMMARY.md

@@ -28,6 +28,8 @@ params {
     // This design ensures explicit per-sample control and eliminates ambiguity.
     // See samplesheet schema and examples in assets/test_data/ for details.
     // ========================================================================
+    num_designs                = null                // Number of intermediate designs (typically specified per-sample in samplesheet)
+    budget                     = null                // Number of final budget designs (typically specified per-sample in samplesheet)
 
     // Boltzgen advanced options
     cache_dir                  = null                // Cache directory for model weights (~6GB), defaults to ~/.cache
@@ -154,7 +156,6 @@ profiles {
 
     docker {
         docker.enabled         = true
-        docker.userEmulation   = true
         podman.enabled         = false
         docker.runOptions = '-u $(id -u):$(id -g)'
     }

nextflow.config

@@ -236,9 +236,14 @@ workflow PROTEIN_DESIGN {
             // Get NPZ and CIF pairs from the conversion step
             ch_ipsae_protenix = CONVERT_PROTENIX_TO_NPZ.out.npz_with_cif
                 .map { meta, npz_file, cif_file ->
-                    // Add source tracking
-                    def ipsae_meta = meta.clone()
-                    ipsae_meta.source = "protenix"
+                    // Add source tracking - create new meta map explicitly to avoid concurrent modification
+                    def ipsae_meta = [
+                        id: meta.id,
+                        parent_id: meta.parent_id,
+                        mpnn_parent_id: meta.mpnn_parent_id,
+                        model_id: meta.model_id,
+                        source: "protenix"
+                    ]
                     [ipsae_meta, npz_file, cif_file]
                 }