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refactor: create standardized Bracken reports
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1 changed files with 23 additions and 2 deletions
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@ -3,8 +3,11 @@
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//
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include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
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include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/krakentools/combinekreports/main'
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include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
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include {
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KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE;
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KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_BRACKEN;
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KRAKENTOOLS_COMBINEKREPORTS
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} from '../../modules/nf-core/krakentools/combinekreports/main'
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include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main'
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include { MOTUS_MERGE } from '../../modules/nf-core/motus/merge/main'
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@ -27,6 +30,7 @@ workflow STANDARDISATION_PROFILES {
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.branch {
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motus: it[0]['tool'] == 'motus'
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kraken2: it[0]['tool'] == 'kraken2'
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bracken: it[0]['tool'] == 'bracken'
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centrifuge: it[0]['tool'] == 'centrifuge'
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metaphlan3: it[0]['tool'] == 'metaphlan3'
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unknown: true
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@ -98,6 +102,23 @@ workflow STANDARDISATION_PROFILES {
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ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS.out.txt )
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ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS.out.versions )
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// Bracken
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// Collect and replace id for db_name for prefix
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// Have to sort by size to ensure first file actually has hits otherwise
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// the script fails
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ch_profiles_for_bracken = ch_input_profiles.bracken
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.map { [it[0]['db_name'], it[1]] }
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.groupTuple(sort: {-it.size()} )
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.map {
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[[id:it[0]], it[1]]
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}
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KRAKENTOOLS_COMBINEKREPORTS_BRACKEN ( ch_profiles_for_bracken )
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ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_BRACKEN.out.txt )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_BRACKEN.out.txt )
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ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS_BRACKEN.out.versions )
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// MetaPhlAn3
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ch_profiles_for_metaphlan3 = ch_input_profiles.metaphlan3
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