Configure PRODIGY pipeline for WES execution with S3 and Harbor

nextflow.config

@@ -0,0 +1,71 @@
+// =============================================================================
+// PRODIGY Nextflow Pipeline Configuration
+// Protein binding affinity prediction from structural data
+// =============================================================================
+
+// Manifest for Nextflow metadata
+manifest {
+    name = 'PRODIGY-Nextflow'
+    author = 'Olamide'
+    homePage = 'https://trs-gitea.cluster.omic.ai/omic/prodigy'
+    description = 'Nextflow pipeline for PRODIGY - Protein binding affinity prediction based on intermolecular contacts'
+    mainScript = 'main.nf'
+    version = '2.4.0'
+}
+
+// Global default parameters
+params {
+    pdb = 's3://omic/eureka/prodigy/input/*.pdb'
+    outdir = 's3://omic/eureka/prodigy/output'
+    distance_cutoff = 5.5
+    acc_threshold = 0.05
+    temperature = 25.0
+    selection = ''
+    contact_list = false
+    pymol_selection = false
+    quiet = false
+}
+
+// Container configurations
+docker {
+    enabled = true
+    runOptions = '-u $(id -u):$(id -g)'
+}
+
+// Process configurations
+process {
+    cpus = 1
+    memory = '4 GB'
+    container = 'harbor.cluster.omic.ai/omic/prodigy:latest'
+}
+
+// Execution configurations
+executor {
+    $local {
+        cpus = 4
+        memory = '8 GB'
+    }
+}
+
+// Profiles for different execution environments
+profiles {
+    standard {
+        docker.enabled = true
+    }
+
+    k8s {
+        docker.enabled = true
+        process.container = 'harbor.cluster.omic.ai/omic/prodigy:latest'
+    }
+
+    k8s_gpu {
+        docker.enabled = true
+        process.container = 'harbor.cluster.omic.ai/omic/prodigy:latest'
+    }
+
+    singularity {
+        singularity.enabled = true
+        singularity.autoMounts = true
+        docker.enabled = false
+    }
+}