init_main.nf

#! /usr/bin/env nextflow

include { db_for_kaiju_pred; create_logf; stdrd_link } from './modules/init/init_conf.nf'
include { stdrd_link as stdrd_link_otfm; stdrd_link as stdrd_link_set} from './modules/init/init_conf.nf'
include { stdrd_link as stdrd_link_tax; stdrd_link as stdrd_link_tax_set; stdrd_link as stdrd_link_info} from './modules/init/init_conf.nf'
include { merge_rvdb_setref; chek_setref_ids; filter_FOI } from './modules/init/filter_rvdb.nf'
include { get_taxonids; get_taxonids_rvdb; set_info_files} from './modules/init/db_taxonomy.nf'
include { taxonomizator; taxonomizator as taxonomizator_rvdb} from './modules/init/db_taxonomy.nf'
include { get_rvdb; get_names_and_nodes;  get_accession2taxid } from './modules/init/update_files.nf' 


if ( params.help ) {
    help = """conf/main.nf: Set up the files for the captvred pipeline run.
             |Required arguments:
             |  --set_seqs  Gziped fasta file with genomic sequences of the species targeted in the TES.
             |  --setname   Name of the set of targeted sequences.
             |              [default: "targetset"]
             |
             |Optional arguments:
             |    --db_update      Force to download rvdb database (in the case it is already downloaded). 
             |                     Most recent version will be always downloaded.
             |                      [default: false]
             |    --merge_update   Force to repeat the merge of reference database and viral candidates sequences if it was already done.
             |                      [default: false] Automatically set to "true" when --taxon_update = true.
             |    --taxon_update   Force to download taxonomic classification files from ncbi (in the case it is already downloaded). 
             |                     Most recent version will be always downloaded.
             |                      [default: false]  Automatically set to "true" when --db_update = true or --taxon_update = true.
             |    
             |Database customization:
             |      
             |      --refdb_link  Database link for downloading desired database for blast (it will be automatically downloaded trough wget). 
             |                      [default: rvdb ]
             |      --kaiju_db    Database(s) to be downloaded for kaiju run. To download multiple dbs use coma separated string. 
             |                      [options: nr_euk, refseqs, viruses, rvdb ]][default: nr_euk ] 
             |                    
    """
    // Print the help with the stripped margin and exit
    println(help)
    exit(0)
}

workflow check_files () {
   take:
      database
      merged
      subset
      
   
   main:

      def do_dbsplit
      def do_merge 
      def do_dbdownl
      if( new File(subset).exists()){
          if (params.dbsplit_update==true) {
            do_dbsplit=true
          }else{
            do_dbsplit=false
          }
      } else {
         do_dbsplit=true
      }


      if( new File(merged).exists()){
          if (params.merge_update==true) {
            do_merge=true
          }else{
            do_merge=false
          }
      } else {
         do_merge=true
      }

      if( new File(database).exists()){
          if (params.db_update==true) {
            do_dbdownl=true
          }else{
            do_dbdownl=false
          }
      } else {
         do_dbdownl=true
      }
  
      if (do_dbdownl==true){
            do_merge=true
      }
      if (do_merge==true){
            do_dbsplit=true
      }

    println "##      FILES CHECKED!     ##"
    println "# Updating database   : $do_dbdownl"
    println "# Mergeing database   : $do_merge"
    println "# Subsetting database : $do_dbsplit"

   emit:
      DWL=do_dbdownl
      MRG=do_merge
      SPT=do_dbsplit

}

workflow database (){
   
   take:
      cond
      dir
      link
      name
      logf
      fasta


   main:
   if (cond){
      get_rvdb(dir, link, name, logf)
      outfl=get_rvdb.out
   } else {
      outfl=fasta
   }
   

   emit:
      outfl

}

workflow mergefasta () {

   take:
      cond
      refseqs_ncbi
      refseqs_rvdb
      db_fa
      set_fa
      merged_fa
      link
      logf

   main:

      if (cond){
         get_names_and_nodes(refseqs_ncbi, link, logf)
         chek_setref_ids(refseqs_rvdb, db_fa, set_fa, params.setname)
         merge_rvdb_setref(merged_fa, db_fa, params.db_name, chek_setref_ids.out, logf )
         out_m=merge_rvdb_setref.out
         out_ncbi=get_names_and_nodes.out
      } else {
         out_m=refseqs_ncbi
         out_ncbi=merged_fa
      }

   emit:
      MERGED=out_m
      NCBID=out_ncbi

}


workflow database_subset (){
   take:
      cond
      rvdbdir
      ncbidir
      bindir
      gffdir
      set_fasta
      fulldb_fasta
      fs 
      os
      link
      logf
      

   main:
      
      stdrd_link_set(set_fasta, "$rvdbdir/setseqs.fasta.gz", logf)
      if (cond) {

         get_accession2taxid(ncbidir, link, logf) 

         get_taxonids(rvdbdir, set_fasta, params.setname, get_accession2taxid.out)
         get_taxonids_rvdb(rvdbdir, fulldb_fasta, get_accession2taxid.out)

         taxonomizator(rvdbdir, get_taxonids.out.TXID, bindir , ncbidir)
         stdrd_link_tax_set(taxonomizator.out, "$rvdbdir/set_tax.tax.gz", logf)
         taxonomizator_rvdb(rvdbdir, get_taxonids_rvdb.out, bindir, ncbidir )
         stdrd_link_tax(taxonomizator_rvdb.out, "$rvdbdir/full_tax.tax.gz", logf)

         set_info_files(get_taxonids.out.GBFL, taxonomizator.out, bindir, gffdir )
         stdrd_link_info(set_info_files.out, "$rvdbdir/info_summary.tsv", logf)
         filter_FOI(rvdbdir, taxonomizator.out, taxonomizator_rvdb.out, fulldb_fasta, bindir )
         
         F=filter_FOI.out.FOI
         O=filter_FOI.out.OTHER
      }else{
         F=fs 
         O=os
      }
      
      
       
      stdrd_link(F, "$rvdbdir/foi_subset_db.fasta.gz", logf)
      stdrd_link_otfm(O, "$rvdbdir/other_subset_db.fasta.gz", logf) 
      

   emit:
      DS_FOI=F
      DS_OTH=O
} 

workflow download_kaijudbs () {
   take:
      odir
      datab
      log_file

   main:
      println "DB is: $datab"
      println "Link is: $params.K_nr_euk_link"
      def link = ":o"
      if (val datab == "nr_euk"){
         link = params.K_nr_euk_link
      } else if (datab == "refseq") {
         link = params.K_refseq_link
      } else if (datab == "viruses") {
         link = params.K_viruses_link
      } else if (datab == "rvdb") {
         link = params.K_rvdb_link
      } else {
         println "WARNING!! Unknown kaiju database! \n Available options are: nr_euk, refseqs, viruses, rvdb"
      }
     println "Link is: $link" 
     db_for_kaiju_pred( odir, link, datab ,log_file )

}

// // // // // // MAIN // // // // // //  
    
    
    println "# Running   : $workflow.scriptId - $workflow.scriptName"
    println "# Project   : $workflow.projectDir"
    println "# Starting  : $workflow.userName  $workflow.start"


workflow {
    def refseqs      = "${workflow.projectDir}/references"
    def refseqs_kai  = "$refseqs/db/kaiju"
    def refseqs_rvdb = "$refseqs/db/${params.refdb_name}"
    def refseqs_gff  = "$refseqs_rvdb/gff_refgenomes"
    def refseqs_ncbi = "$refseqs/db/ncbi"
   
    def bindir       = "${workflow.projectDir}/bin"

    def rvdb_fa      = "${refseqs_rvdb}/${params.db_name}"
    def merged_fa    = "${refseqs_rvdb}/rvdb+${params.setname}.fasta.gz"
    def rvdb_tax     = "${refseqs_rvdb}/rvdb+${params.setname}.tax"
    def foisubset    = "${refseqs_rvdb}/rvdb+${params.setname}_foi_subset.fasta.gz"
    def othersubset  = "${refseqs_rvdb}/rvdb+${params.setname}_other_subset.fasta.gz"
    
        check_files(rvdb_fa, merged_fa, foisubset)

        create_logf(refseqs)
        def log_file=create_logf.out

        database( check_files.out.DWL,
                      refseqs_rvdb, 
                      params.rvdb_link, 
                      params.db_name, 
                      log_file, 
                      rvdb_fa
                    )

         mergefasta( check_files.out.MRG,
                        refseqs_ncbi, 
                        refseqs_rvdb, 
                        database.out,
                        params.set_seqs, 
                        merged_fa, 
                        params.taxon_link, 
                        create_logf.out
                     )

         database_subset( check_files.out.SPT,
                          refseqs_rvdb, 
                          mergefasta.out.NCBID, 
                          bindir, 
                          refseqs_gff,
                          params.set_seqs, 
                          mergefasta.out.MERGED,
                          foisubset,
                          othersubset,
                          params.acc2tax_link,
                          create_logf.out
                     )

   if (params.customdb) {
            db_for_kaiju(params.dbtomake, log_file)
            println "AAAAAA"
         } else {
            println "EEEEEE"
            def kaidatabases=Channel.from(params.kaiju_db)
               .splitCsv()
               .flatten()
            println "$refseqs_kai"
           // download_kaijudbs(refseqs_kai, Channel.from(params.kaiju_db).splitCsv().flatten() , log_file )
           // download_kaijudbs(refseqs_kai, kaidatabases, log_file )
         db_for_kaiju_pred(refseqs_kai, kaidatabases, log_file )
         }
}