Initial commit: FlowDock pipeline configured for WES execution

main.nf

@@ -0,0 +1,74 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+params.input_receptor = 'YNKIVHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNKLEGKVPMHKLFLEMLEAKV'
+params.input_ligand = 'c1cc2c(cc1O)CCCC2'
+params.input_template = ''
+params.sample_id = 'flowdock_sample'
+params.outdir = 's3://omic/eureka/flowdock/output/'
+params.n_samples = 5
+
+process FLOWDOCK {
+    container 'harbor.cluster.omic.ai/omic/flowdock:latest'
+    containerOptions '--rm --gpus all'
+    publishDir params.outdir, mode: 'copy'
+    stageInMode 'copy'
+
+    input:
+        val receptor
+        val ligand
+
+    output:
+        path "${params.sample_id}/*.pdb", optional: true
+        path "${params.sample_id}/*.sdf", optional: true
+        path "${params.sample_id}/**/*.pdb", optional: true
+        path "run.log"
+
+    script:
+        """
+        set +u
+        source /opt/conda/etc/profile.d/conda.sh
+        conda activate FlowDock
+        
+        mkdir -p ${params.sample_id}
+
+        python /software/flowdock/flowdock/sample.py \\
+            ckpt_path=/software/flowdock/checkpoints/esmfold_prior_paper_weights-EMA.ckpt \\
+            model.cfg.prior_type=esmfold \\
+            sampling_task=batched_structure_sampling \\
+            input_receptor='${receptor}' \\
+            input_ligand='"${ligand}"' \\
+            ${params.input_template ? "input_template=${params.input_template}" : "input_template=null"} \\
+            sample_id='${params.sample_id}' \\
+            out_path=\$PWD/${params.sample_id}/ \\
+            paths.output_dir=\$PWD/${params.sample_id}/ \\
+            hydra.run.dir=\$PWD/${params.sample_id}/ \\
+            n_samples=${params.n_samples} \\
+            chunk_size=5 \\
+            num_steps=40 \\
+            sampler=VDODE \\
+            sampler_eta=1.0 \\
+            start_time='1.0' \\
+            use_template=true \\
+            separate_pdb=true \\
+            visualize_sample_trajectories=false \\
+            auxiliary_estimation_only=false \\
+            esmfold_chunk_size=null \\
+            trainer=gpu 2>&1 | tee run.log
+        
+        # Copy any outputs from FlowDock's log directory if they exist there
+        if ls /software/flowdock/logs/sample/runs/*/rank*.pdb 2>/dev/null; then
+            cp /software/flowdock/logs/sample/runs/*/rank*.pdb ${params.sample_id}/ 2>/dev/null || true
+            cp /software/flowdock/logs/sample/runs/*/rank*.sdf ${params.sample_id}/ 2>/dev/null || true
+        fi
+        
+        # List what was generated
+        echo "=== Generated files ===" >> run.log
+        find ${params.sample_id}/ -type f >> run.log 2>&1 || true
+        """
+}
+
+workflow {
+    FLOWDOCK(Channel.of(params.input_receptor), Channel.of(params.input_ligand))
+}