Configure PRODIGY pipeline for WES execution with S3 and Harbor

main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+// Default parameters
+params.pdb = 's3://omic/eureka/prodigy/input/*.pdb'
+params.outdir = 's3://omic/eureka/prodigy/output'
+params.distance_cutoff = 5.5
+params.acc_threshold = 0.05
+params.temperature = 25.0
+params.selection = ''
+params.contact_list = false
+params.pymol_selection = false
+params.quiet = false
+
+// =============================================================================
+// Process: PRODIGY
+// Predicts binding affinity using intermolecular contacts
+// =============================================================================
+
+process PRODIGY {
+    container 'harbor.cluster.omic.ai/omic/prodigy:latest'
+    publishDir params.outdir, mode: 'copy'
+    stageInMode 'copy'
+
+    input:
+        path pdb
+
+    output:
+        path "${pdb.baseName}_prodigy.txt", emit: results
+        path "${pdb.baseName}_contacts.txt", optional: true, emit: contacts
+        path "${pdb.baseName}_interface.pml", optional: true, emit: pymol
+
+    script:
+        """
+        prodigy \\
+            ${pdb} \\
+            --distance-cutoff ${params.distance_cutoff} \\
+            --acc-threshold ${params.acc_threshold} \\
+            --temperature ${params.temperature} \\
+            ${params.selection ? '--selection ' + params.selection : ''} \\
+            ${params.contact_list ? '--contact_list' : ''} \\
+            ${params.pymol_selection ? '--pymol_selection' : ''} \\
+            ${params.quiet ? '--quiet' : ''} \\
+            2>&1 | tee ${pdb.baseName}_prodigy.txt
+
+        # Rename contact list file if generated
+        if [ -f "${pdb.baseName}.contacts" ]; then
+            mv ${pdb.baseName}.contacts ${pdb.baseName}_contacts.txt
+        fi
+
+        # Rename PyMOL script if generated
+        if [ -f "${pdb.baseName}.pml" ]; then
+            mv ${pdb.baseName}.pml ${pdb.baseName}_interface.pml
+        fi
+        """
+}
+
+// =============================================================================
+// Workflow
+// =============================================================================
+
+workflow {
+    // Validate input
+    if (!params.pdb) {
+        error "ERROR: Please provide input PDB file(s) using --pdb parameter"
+    }
+
+    // Create input channel
+    pdb_ch = Channel.fromPath(params.pdb, checkIfExists: true)
+
+    // Run PRODIGY
+    PRODIGY(pdb_ch)
+}