diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index 5e2a7d2..e76db6c 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -41,7 +41,7 @@ workflow PROFILING { .combine(databases) .branch { malt: it[2]['tool'] == 'malt' - kraken2: it[2]['tool'].contains('kraken2') + kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' metaphlan3: it[2]['tool'] == 'metaphlan3' centrifuge: it[2]['tool'] == 'centrifuge' kaiju: it[2]['tool'] == 'kaiju' @@ -133,7 +133,7 @@ workflow PROFILING { ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment ) ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report - // Set the tool to be strictly 'kraken2' instead of potentially 'kraken2+bracken' for downstream use. + // Set the tool to be strictly 'kraken2' instead of potentially 'bracken' for downstream use. .map { meta, report -> [meta + [tool: 'kraken2'], report]} ) @@ -142,7 +142,7 @@ workflow PROFILING { if ( params.run_kraken2 && params.run_bracken ) { def ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report - .filter { meta, report -> meta['tool'].contains('bracken') } + .filter { meta, report -> meta['tool'] == 'bracken' } if (params.kraken2_save_minimizers) { ch_input_for_bracken = KRAKEN2_STANDARD_REPORT(ch_input_for_bracken).report @@ -151,21 +151,17 @@ workflow PROFILING { ch_input_for_bracken = ch_input_for_bracken .combine( databases.filter { meta, db -> - meta['tool'].contains('bracken') + meta['tool'] == 'bracken' } ) .multiMap { meta, report, db_meta, db -> - report: [meta, report] + report: [meta + db_meta, report] db: db } BRACKEN_BRACKEN(ch_input_for_bracken.report, ch_input_for_bracken.db) ch_versions = ch_versions.mix(BRACKEN_BRACKEN.out.versions.first()) - ch_raw_profiles = ch_raw_profiles.mix( - BRACKEN_BRACKEN.out.reports - // Set the tool to be strictly 'bracken' instead of potentially 'kraken2+bracken' for downstream use. - .map { meta, report -> [meta + [tool: 'bracken'], report]} - ) + ch_raw_profiles = ch_raw_profiles.mix(BRACKEN_BRACKEN.out.reports) }