67 lines
2.6 KiB
Plaintext
67 lines
2.6 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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params.pdb = 's3://omic/eureka/ligandmpnn/1BC8'
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params.outdir = 's3://omic/eureka/ligandmpnn/output'
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params.model_type = 'ligand_mpnn'
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params.temperature = 0.1
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params.seed = 111
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params.batch_size = 1
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params.number_of_batches = 1
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params.chains_to_design = ''
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params.fixed_residues = ''
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params.pack_side_chains = 0
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process LIGANDMPNN {
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container 'harbor.cluster.omic.ai/omic/ligandmpnn: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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path pdb
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output:
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path "${pdb.simpleName}/seqs/*.fa"
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path "${pdb.simpleName}/backbones/*.pdb"
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path "${pdb.simpleName}/packed/*.pdb", optional: true
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path "run.log"
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script:
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// Set checkpoint path based on model type
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def checkpoint_arg = ''
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if (params.model_type == 'ligand_mpnn') {
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checkpoint_arg = '--checkpoint_ligand_mpnn /app/LigandMPNN/model_params/ligandmpnn_v_32_010_25.pt'
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} else if (params.model_type == 'protein_mpnn') {
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checkpoint_arg = '--checkpoint_protein_mpnn /app/LigandMPNN/model_params/proteinmpnn_v_48_020.pt'
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} else if (params.model_type == 'soluble_mpnn') {
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checkpoint_arg = '--checkpoint_soluble_mpnn /app/LigandMPNN/model_params/solublempnn_v_48_020.pt'
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} else if (params.model_type == 'global_label_membrane_mpnn') {
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checkpoint_arg = '--checkpoint_global_label_membrane_mpnn /app/LigandMPNN/model_params/global_label_membrane_mpnn_v_48_020.pt'
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} else if (params.model_type == 'per_residue_label_membrane_mpnn') {
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checkpoint_arg = '--checkpoint_per_residue_label_membrane_mpnn /app/LigandMPNN/model_params/per_residue_label_membrane_mpnn_v_48_020.pt'
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}
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"""
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mkdir -p ${pdb.simpleName}/seqs ${pdb.simpleName}/backbones ${pdb.simpleName}/packed
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ligandmpnn \\
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--pdb_path \$PWD/${pdb} \\
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--out_folder \$PWD/${pdb.simpleName} \\
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--model_type ${params.model_type} \\
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${checkpoint_arg} \\
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--temperature ${params.temperature} \\
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--seed ${params.seed} \\
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--batch_size ${params.batch_size} \\
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--number_of_batches ${params.number_of_batches} \\
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--pack_side_chains ${params.pack_side_chains} \\
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${params.chains_to_design ? "--chains_to_design ${params.chains_to_design}" : ''} \\
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${params.fixed_residues ? "--fixed_residues \"${params.fixed_residues}\"" : ''} \\
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2>&1 | tee run.log
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"""
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}
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workflow {
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LIGANDMPNN(Channel.fromPath(params.pdb))
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}
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