// // Remove host reads via alignment and export off-target reads // include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main' include { KRONA_CLEANUP as KRONA_KRAKENCLEANUP } from '../../modules/local/krona_cleanup' include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/modules/krona/ktimporttext/main' include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main' workflow POSTPROCESSING_KRONA { take: krona_input databases main: ch_versions = Channel.empty() ch_input_for_ktimporttext = Channel.empty() ch_files_for_krona = krona_input .branch { // malt: kraken2: it[0]['tool'] == 'kraken2' centrifuge: it[0]['tool'] == 'centrifuge' //metaphlan3: //kaiju: //diamond: } ch_databases = databases .branch{ centrifuge: it[0]['tool'] == 'centrifuge' } // TODO PUSH BACK CENTRIFUGE_KREPORT TO PROFILING.NF WHERE DATABASE ALREADY IS? ch_input_for_centrifuge_kreport = ch_files_for_krona.centrifuge .dump(tag: "db_for_kreport_pre") .join(ch_databases, by: 0) .dump(tag: "db_for_kreport_post") // Kraken KRAKENTOOLS_KREPORT2KRONA ( ch_files_for_krona.kraken2 ) KRONA_KRAKENCLEANUP ( KRAKENTOOLS_KREPORT2KRONA.out.txt ) ch_kraken_for_krona = KRONA_KRAKENCLEANUP.out.txt .map{ [[id: it[0].tool + "-" + it[0].db_name, db_name: it[0].db_name, tool: it[0].tool ], it[1]] } .groupTuple() ch_input_for_ktimporttext = ch_input_for_ktimporttext.mix( ch_kraken_for_krona ) ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() ) ch_versions = ch_versions.mix( KRONA_KRAKENCLEANUP.out.versions.first() ) KRONA_KTIMPORTTEXT (ch_input_for_ktimporttext) ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() ) // Centrifuge //CENTRIFUGE_KREPORT (krona_input.centrifuge, ch_input_for_centrifuge.db) // ch_versions = ch_versions.mix( /CENTRIFUGE_KREPORT.out.versions.first() ) emit: versions = ch_versions // channel: [ versions.yml ] }