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Merge pull request #94 from MillironX/feature/centrifuge2krona

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Add Krona output for Centrifuge profiles
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James A. Fellows Yates 2022-06-27 17:13:31 +02:00 committed by GitHub
commit e66c2b9b87
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subworkflows/local/visualization_krona.nf
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@ -20,6 +20,7 @@ workflow VISUALIZATION_KRONA {
*/ */
ch_input_profiles = profiles ch_input_profiles = profiles
.branch { .branch {
centrifuge: it[0]['tool'] == 'centrifuge'
kraken2: it[0]['tool'] == 'kraken2' kraken2: it[0]['tool'] == 'kraken2'
unknown: true unknown: true
} }
@ -28,6 +29,7 @@ workflow VISUALIZATION_KRONA {
Convert Kraken2 formatted reports into Krona text files Convert Kraken2 formatted reports into Krona text files
*/ */
ch_kraken_reports = ch_input_profiles.kraken2 ch_kraken_reports = ch_input_profiles.kraken2
.mix( ch_input_profiles.centrifuge )
KRAKENTOOLS_KREPORT2KRONA ( ch_kraken_reports ) KRAKENTOOLS_KREPORT2KRONA ( ch_kraken_reports )
ch_krona_text = ch_krona_text.mix( KRAKENTOOLS_KREPORT2KRONA.out.txt ) ch_krona_text = ch_krona_text.mix( KRAKENTOOLS_KREPORT2KRONA.out.txt )
ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() ) ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )