#!/usr/bin/env nextflow

nextflow.enable.dsl=2

params.pdb = null
params.outdir = null
params.ph = 7.0
params.options = ""

process PROPKA {
    container 'harbor.cluster.omic.ai/omic/propka:latest'
    publishDir params.outdir, mode: 'copy'
    stageInMode 'copy'

    input:
        path pdb

    output:
        path "${pdb.baseName}.pka", emit: pka_file
        path "run.log"

    script:
        """
        propka3 ${params.options} --pH ${params.ph} ${pdb} 2>&1 | tee run.log
        """
}

workflow {
    pdb_files = Channel.fromPath(params.pdb)
    PROPKA(pdb_files)
}