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