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

2026-03-17 17:57:24 +01:00
commit 6eef3bb748
108 changed files with 28144 additions and 0 deletions
--- a/main.nf
+++ b/main.nf
@@ -0,0 +1,121 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+// Input parameters
+params.protein_fasta = 's3://omic/eureka/rosettafold-all-atom/input/protein.fasta'
+params.na_fasta = ''
+params.na_type = 'dna'
+params.sm_file = ''
+params.sm_type = 'sdf'
+params.covale_inputs = ''
+
+// Output parameters
+params.outdir = 's3://omic/eureka/rosettafold-all-atom/output'
+params.job_name = 'rfaa_prediction'
+
+// Model parameters
+params.max_cycle = 4
+
+// Database parameters
+params.db_uniref30 = '/mnt/databases/UniRef30_2020_06'
+params.db_bfd = '/mnt/databases/bfd'
+params.db_pdb100 = '/mnt/databases/pdb100_2021Mar03'
+params.weights = '/mnt/databases/RFAA_paper_weights.pt'
+
+process RFAA_PREDICT {
+    container 'harbor.cluster.omic.ai/omic/rosettafold-all-atom:latest'
+    containerOptions '--rm --gpus all -v /mnt:/mnt'
+    publishDir params.outdir, mode: 'copy'
+    stageInMode 'copy'
+
+    input:
+        path protein_fasta
+
+    output:
+        path "${params.job_name}.pdb"
+        path "${params.job_name}_aux.pt"
+        path "run.log"
+
+    script:
+        def na_block = params.na_fasta ? """
+na_inputs:
+  B:
+    fasta: ${params.na_fasta}
+    input_type: "${params.na_type}"
+""" : ""
+        def sm_block = params.sm_file ? """
+sm_inputs:
+  C:
+    input: ${params.sm_file}
+    input_type: "${params.sm_type}"
+""" : ""
+        def covale_block = params.covale_inputs ? """
+covale_inputs: "${params.covale_inputs}"
+""" : ""
+        """
+        mkdir -p config
+
+        # Create hydra config file
+        cat > config/${params.job_name}.yaml << EOF
+defaults:
+  - base
+
+job_name: "${params.job_name}"
+
+protein_inputs:
+  A:
+    fasta_file: \$PWD/${protein_fasta}
+${na_block}${sm_block}${covale_block}
+loader_params:
+  MAXCYCLE: ${params.max_cycle}
+EOF
+
+        # Create base config with database paths
+        cat > config/base.yaml << EOF
+output_path: "."
+
+database_params:
+  sequencedb: "${params.db_pdb100}/pdb100_2021Mar03"
+  hhdb: "${params.db_pdb100}/pdb100_2021Mar03"
+  command: "/opt/RoseTTAFold-All-Atom/make_msa.sh"
+
+checkpoint_path: "${params.weights}"
+
+loader_params:
+  MAXCYCLE: ${params.max_cycle}
+
+model_params:
+  n_extra_block: 4
+  n_main_block: 32
+  n_ref_block: 4
+  d_msa: 256
+  d_msa_full: 64
+  d_pair: 128
+  d_templ: 64
+  n_head_msa: 8
+  n_head_pair: 4
+  n_head_templ: 4
+  d_hidden: 32
+  d_hidden_templ: 32
+  p_drop: 0.0
+EOF
+
+        # Set environment variables
+        export DB_UR30="${params.db_uniref30}/UniRef30_2020_06"
+        export DB_BFD="${params.db_bfd}/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt"
+        export BLASTMAT="/opt/RoseTTAFold-All-Atom/blast-2.2.26/data/"
+
+        # Run RFAA
+        cd /opt/RoseTTAFold-All-Atom
+        python -m rf2aa.run_inference \
+            --config-path \$OLDPWD/config \
+            --config-name ${params.job_name} 2>&1 | tee \$OLDPWD/run.log
+
+        cd \$OLDPWD
+        """
+}
+
+workflow {
+    RFAA_PREDICT(Channel.fromPath(params.protein_fasta))
+}