params.config.in

import java.time.*
Date now = new Date()
params.timestamp = now.format("yyyyMMdd-HH:mm:ss")

params {
        runID                   = now.format("yyyyMMdd-HH:mm:ss")

        // input
        data                    = ""

        alphafold               = "no"
        ref_files               = "$params.data"

        tools                   = "diffdock,tankbind,vina,smina,gnina"          // diffdock,tankbind,vina,smina,gnina,edmdock

        // pipeline options
        ligand_preprocessing    = "yes"         // yes, no
        receptor_Hs             = "no"          // yes, no
        p2rank_only             = "no"          // yes, no
        diffdock_mode           = "batch"       // batch, single

        scoring_receptors       = "no"          // yes, no
        scoring_ligands         = "yes"         // yes, no

        // parameters
        autobox_add             = "10"
        vina_params             = "--exhaustiveness=64 --seed 160490"
        smina_params            = "--exhaustiveness=64 --seed 160490"
        gnina_params            = "--exhaustiveness=64 --seed 160490"
        diffdock_params         = "--inference_steps 20 --samples_per_complex 40 --batch_size 10 --actual_steps 18 --no_final_step_noise"

        // tool locations
        diffdock_tool           = "<path to DiffDock directory>"
        vina_tool               = "<path to vina executable>"
        p2rank_tool             = "<path to p2rank>"
        tankbind_scripts        = "$baseDir/bin/tankbind/"
        edmdock_tool            = "<path to EDMDock directory>"

        // conda containers
        diffdock_conda          = "<path to DiffDock conda env>"
        meeko_conda             = "<path to Meeko conda env>"
        vina_conda              = "<path to Autodock Vina conda env>"
        smina_conda             = "<path to SMINA conda env>"
        pdbfixer_conda          = "<path to PDBFixer conda env>"
        edmdock_conda           = "<path to EDMDock conda env>"

        // singularity images
        tankbind_sing           = "<path to TANKBind Singularity img>"
        gnina_sing              = "<path to GNINA Singularity img>"
        adfr_sing               = "<path to ADFR Singularity img>"
        ost_sing                = "<path to OpenStrucutre Singularity img>"

        // load java
        load_java               = "<command to enable java>"

        // cluster options: define queues, partions, ... ; anything besides time and memory
        cpu_options             = "<slurm cluster options for cpu processes>"
        diffdock_options        = "<slurm cluster options for DiffDock>"
        gnina_options           = "<slurm cluster options for GNINA>"
        edmdock_options         = "<slurm cluster options for EDMDock>"
}