propka/main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl=2

params.pdb = "/mnt/OmicNAS/private/old/olamide/propka/input/1HPX.pdb"
params.outdir = "/mnt/OmicNAS/private/old/olamide/propka/output"
params.ph = 7.0
params.options = ""

process PROPKA {
    container 'propka:latest'
    publishDir params.outdir, mode: '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)
}