omic
da8af7bbc3
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74 lines
2.7 KiB
Plaintext
74 lines
2.7 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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params.input_receptor = 'YNKIVHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNKLEGKVPMHKLFLEMLEAKV'
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params.input_ligand = 'c1cc2c(cc1O)CCCC2'
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params.input_template = ''
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params.sample_id = 'flowdock_sample'
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params.outdir = 's3://omic/eureka/flowdock/output/'
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params.n_samples = 5
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process FLOWDOCK {
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container 'harbor.cluster.omic.ai/omic/flowdock:latest'
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publishDir params.outdir, mode: 'copy'
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stageInMode 'copy'
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input:
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val receptor
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val ligand
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output:
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path "${params.sample_id}/*.pdb", optional: true
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path "${params.sample_id}/*.sdf", optional: true
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path "${params.sample_id}/**/*.pdb", optional: true
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path "run.log"
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script:
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"""
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set +u
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source /opt/conda/etc/profile.d/conda.sh
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conda activate FlowDock
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mkdir -p ${params.sample_id}
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python /software/flowdock/flowdock/sample.py \\
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ckpt_path=/software/flowdock/checkpoints/esmfold_prior_paper_weights-EMA.ckpt \\
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model.cfg.prior_type=esmfold \\
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sampling_task=batched_structure_sampling \\
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input_receptor='${receptor}' \\
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input_ligand='"${ligand}"' \\
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${params.input_template ? "input_template=${params.input_template}" : "input_template=null"} \\
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sample_id='${params.sample_id}' \\
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out_path=\$PWD/${params.sample_id}/ \\
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paths.output_dir=\$PWD/${params.sample_id}/ \\
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hydra.run.dir=\$PWD/${params.sample_id}/ \\
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n_samples=${params.n_samples} \\
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chunk_size=5 \\
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num_steps=40 \\
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sampler=VDODE \\
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sampler_eta=1.0 \\
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start_time='1.0' \\
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use_template=true \\
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separate_pdb=true \\
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visualize_sample_trajectories=false \\
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auxiliary_estimation_only=false \\
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esmfold_chunk_size=null \\
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trainer=gpu 2>&1 | tee run.log
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# Copy any outputs from FlowDock's log directory if they exist there
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if ls /software/flowdock/logs/sample/runs/*/rank*.pdb 2>/dev/null; then
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cp /software/flowdock/logs/sample/runs/*/rank*.pdb ${params.sample_id}/ 2>/dev/null || true
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cp /software/flowdock/logs/sample/runs/*/rank*.sdf ${params.sample_id}/ 2>/dev/null || true
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fi
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# List what was generated
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echo "=== Generated files ===" >> run.log
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find ${params.sample_id}/ -type f >> run.log 2>&1 || true
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"""
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}
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workflow {
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FLOWDOCK(Channel.of(params.input_receptor), Channel.of(params.input_ligand))
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}
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