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106 lines
3.8 KiB
Plaintext
106 lines
3.8 KiB
Plaintext
//
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// Create Krona visualizations
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//
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include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_KRONA } from '../../modules/nf-core/megan/rma2info/main'
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include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/kaiju/kaiju2krona/main'
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include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/krakentools/kreport2krona/main'
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include { KRONA_CLEANUP } from '../../modules/local/krona_cleanup'
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include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/krona/ktimporttext/main'
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include { KRONA_KTIMPORTTAXONOMY } from '../../modules/nf-core/krona/ktimporttaxonomy/main'
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include { GUNZIP } from '../../modules/nf-core/gunzip/main'
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workflow VISUALIZATION_KRONA {
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take:
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classifications
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profiles
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databases
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main:
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ch_krona_text = Channel.empty()
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ch_krona_html = Channel.empty()
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ch_versions = Channel.empty()
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/*
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Split profile results based on tool they come from
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*/
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ch_input_profiles = profiles
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.branch {
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centrifuge: it[0]['tool'] == 'centrifuge'
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kraken2: it[0]['tool'] == 'kraken2'
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unknown: true
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}
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ch_input_classifications = classifications
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.branch {
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kaiju: it[0]['tool'] == 'kaiju'
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malt: it[0]['tool'] == 'malt'
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unknown: true
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}
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/*
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Convert Kraken2 formatted reports into Krona text files
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*/
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ch_kraken_reports = ch_input_profiles.kraken2
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.mix( ch_input_profiles.centrifuge )
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KRAKENTOOLS_KREPORT2KRONA ( ch_kraken_reports )
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ch_krona_text = ch_krona_text.mix( KRAKENTOOLS_KREPORT2KRONA.out.txt )
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ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
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/*
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Combine Kaiju profiles with their databases
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*/
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ch_input_for_kaiju2krona = ch_input_classifications.kaiju
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.map{ [it[0]['db_name'], it[0], it[1]] }
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.combine( databases.map{ [it[0]['db_name'], it[1]] }, by: 0 )
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.multiMap{
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it ->
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profiles: [it[1], it[2]]
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db: it[3]
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}
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/*
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Convert Kaiju formatted reports into Krona text files
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*/
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KAIJU_KAIJU2KRONA( ch_input_for_kaiju2krona.profiles, ch_input_for_kaiju2krona.db )
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ch_krona_text = ch_krona_text.mix( KAIJU_KAIJU2KRONA.out.txt )
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ch_versions = ch_versions.mix( KAIJU_KAIJU2KRONA.out.versions.first() )
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/*
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Remove taxonomy level annotations from the Krona text files
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*/
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KRONA_CLEANUP( ch_krona_text )
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ch_cleaned_krona_text = KRONA_CLEANUP.out.txt
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ch_versions = ch_versions.mix( KRONA_CLEANUP.out.versions.first() )
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/*
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Convert Krona text files into html Krona visualizations
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*/
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ch_krona_text_for_import = ch_cleaned_krona_text
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.map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]}
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.groupTuple()
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KRONA_KTIMPORTTEXT( ch_krona_text_for_import )
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ch_krona_html = ch_krona_html.mix( KRONA_KTIMPORTTEXT.out.html )
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ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
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/*
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Convert MALT/MEGAN RMA2INFO files into html Krona visualisations
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*/
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if ( params.krona_taxonomy_directory ) {
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MEGAN_RMA2INFO_KRONA ( ch_input_classifications.malt, false )
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GUNZIP ( MEGAN_RMA2INFO_KRONA.out.txt )
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ch_krona_taxonomy_for_input = GUNZIP.out.gunzip
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.map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]}
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.groupTuple()
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KRONA_KTIMPORTTAXONOMY ( ch_krona_taxonomy_for_input, file(params.krona_taxonomy_directory, checkExists: true) )
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ch_krona_html.mix( KRONA_KTIMPORTTAXONOMY.out.html )
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ch_versions = ch_versions.mix( MEGAN_RMA2INFO_KRONA.out.versions.first() )
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ch_versions = ch_versions.mix( KRONA_KTIMPORTTAXONOMY.out.versions.first() )
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}
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emit:
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html = ch_krona_html
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versions = ch_versions
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}
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