main.nf

#!/usr/bin/env nextflow
import groovy.json.JsonSlurper
// params.projectDir = "/data1/choderaj/paynea/plumb/rough-drafts/20250325_initial_scripts_w_nextflow"
params.projectDir = "/home/brennera/mystore/code/nf-core-plumb/"
params.scripts = "${params.projectDir}/bin"
// params.bindingDB = "/data1/choderaj/paynea/plumb_binding_db/BindingDBValidationSets-1/test"
params.bindingDB = "/home/brennera/mystore/data/bind_db/testing_subset"

// hacky way to get around needing to learn to read FASTA from cif
params.fasta = "MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL"
// this being hard coded is bad but it should be easy to automate tying this sdf file to the uuid and then each one can be passed separately
params.congenericSeries = "${params.bindingDB}/1YKR_Validation_Affinities_3D.sdf"

// this should eventually be split out to be more helpful
params.output = "${params.projectDir}/output"

// Conda Envs
// params.asap = "/home/paynea/miniforge3/envs/asap2025"
params.asap = "/home/brennera/miniconda3/envs/asapdiscovery"

// Flags
params.take = -1

/*
 * Define the workflow
 */
include {
PROCESS_BINDINGDB;
DOWNLOAD_PDB;
PREP_CIF;
PREP_FOR_DOCKING;
ASSESS_PREPPED_PROTEIN;
GENERATE_CONSTRAINED_LIGAND_POSES;
MAKE_FEC_INPUTS;
VISUALIZE_NETWORK;
} from "./modules.nf"

workflow {
    // Output is only written into the work directory, not saved anywhere obvious
    PROCESS_BINDINGDB()
    input_files = PROCESS_BINDINGDB.out.input_json.flatten().take(params.take)

    // Load in input json files and extract unique id from each and connect it to the json
    input_files.map{json ->  tuple([new JsonSlurper().parseText(json.text)][0].get("BindingDB monomerid"), json)}
        .set{unique_jsons}
    // Spruce is not compatible with the file I download
    DOWNLOAD_PDB(unique_jsons)
    PREP_CIF(DOWNLOAD_PDB.out.input_cif.combine(DOWNLOAD_PDB.out.record_json, by:0))
    // Use ASAP CLI to prepare the protein for docking
    PREP_FOR_DOCKING(PREP_CIF.out.prepped_pdb)
    // Generate a quality report using Open Eye tools
    ASSESS_PREPPED_PROTEIN(PREP_FOR_DOCKING.out.design_unit)
    // Use ASAP tools to generate constrained ligand poses 
    GENERATE_CONSTRAINED_LIGAND_POSES(PREP_FOR_DOCKING.out.json_schema)
    // Use ASAP alchemy CLI
    MAKE_FEC_INPUTS(GENERATE_CONSTRAINED_LIGAND_POSES.out.posed_ligands.combine(PREP_FOR_DOCKING.out.prepped_pdb, by:0))
    // Visualize the network using OpenFE tools
    VISUALIZE_NETWORK(MAKE_FEC_INPUTS.out.network_graph)
}