Initial commit: RoseTTAFold-All-Atom configured for Wes with Harbor images and s3:// paths

nextflow.config

@@ -0,0 +1,66 @@
+// Manifest for Nextflow metadata
+manifest {
+    name = 'RoseTTAFold-All-Atom'
+    author = 'Baker Laboratory'
+    homePage = 'https://github.com/baker-laboratory/RoseTTAFold-All-Atom'
+    description = 'Nextflow pipeline for RoseTTAFold-All-Atom biomolecular structure prediction'
+    mainScript = 'main.nf'
+    version = '1.0.0'
+}
+
+// Global default parameters
+params {
+    // Input files
+    protein_fasta = "s3://omic/eureka/rosettafold-all-atom/input/protein.fasta"
+    na_fasta = ""
+    na_type = "dna"
+    sm_file = ""
+    sm_type = "sdf"
+    covale_inputs = ""
+
+    // Output
+    outdir = "s3://omic/eureka/rosettafold-all-atom/output"
+    job_name = "rfaa_prediction"
+
+    // Model settings
+    max_cycle = 4
+
+    // Database paths
+    db_uniref30 = "/mnt/databases/UniRef30_2020_06"
+    db_bfd = "/mnt/databases/bfd"
+    db_pdb100 = "/mnt/databases/pdb100_2021Mar03"
+    weights = "/mnt/databases/RFAA_paper_weights.pt"
+}
+
+// Container configurations
+docker {
+    enabled = true
+    runOptions = '--gpus all'
+}
+
+// Process configurations
+process {
+    cpus = 8
+    memory = '64 GB'
+}
+
+// Execution configurations
+executor {
+    $local {
+        cpus = 16
+        memory = '64 GB'
+    }
+}
+
+// Profiles
+profiles {
+    k8s {
+        process {
+            container = 'harbor.cluster.omic.ai/omic/rosettafold-all-atom:latest'
+        }
+        docker {
+            enabled = true
+            runOptions = '--gpus all'
+        }
+    }
+}