Olamide Isreal
c8fd6b4084
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75 lines
2.3 KiB
Plaintext
75 lines
2.3 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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// Default parameters
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params.pdb = 's3://omic/eureka/prodigy/*.pdb'
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params.outdir = 's3://omic/eureka/prodigy/output'
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params.distance_cutoff = 5.5
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params.acc_threshold = 0.05
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params.temperature = 25.0
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params.selection = ''
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params.contact_list = false
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params.pymol_selection = false
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params.quiet = false
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// =============================================================================
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// Process: PRODIGY
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// Predicts binding affinity using intermolecular contacts
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// =============================================================================
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process PRODIGY {
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container 'harbor.cluster.omic.ai/omic/prodigy: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 "${pdb.baseName}_prodigy.txt", emit: results
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path "${pdb.baseName}_contacts.txt", optional: true, emit: contacts
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path "${pdb.baseName}_interface.pml", optional: true, emit: pymol
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script:
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"""
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prodigy \\
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${pdb} \\
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--distance-cutoff ${params.distance_cutoff} \\
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--acc-threshold ${params.acc_threshold} \\
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--temperature ${params.temperature} \\
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${params.selection ? '--selection ' + params.selection : ''} \\
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${params.contact_list ? '--contact_list' : ''} \\
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${params.pymol_selection ? '--pymol_selection' : ''} \\
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${params.quiet ? '--quiet' : ''} \\
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2>&1 | tee ${pdb.baseName}_prodigy.txt
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# Rename contact list file if generated
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if [ -f "${pdb.baseName}.contacts" ]; then
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mv ${pdb.baseName}.contacts ${pdb.baseName}_contacts.txt
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fi
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# Rename PyMOL script if generated
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if [ -f "${pdb.baseName}.pml" ]; then
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mv ${pdb.baseName}.pml ${pdb.baseName}_interface.pml
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fi
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"""
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}
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// =============================================================================
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// Workflow
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// =============================================================================
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workflow {
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// Validate input
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if (!params.pdb) {
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error "ERROR: Please provide input PDB file(s) using --pdb parameter"
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}
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// Create input channel
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pdb_ch = Channel.fromPath(params.pdb, checkIfExists: true)
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// Run PRODIGY
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PRODIGY(pdb_ch)
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}
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