From 8deb7757d8a260fb2bc4c5890a10995181d1bafe Mon Sep 17 00:00:00 2001 From: "Moritz E. Beber" Date: Wed, 19 Oct 2022 16:21:57 +0200 Subject: [PATCH] fix: remove Bracken from standardise reports --- .../local/standardisation_profiles.nf | 25 ++----------------- 1 file changed, 2 insertions(+), 23 deletions(-) diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf index f560424..cbb0fab 100644 --- a/subworkflows/local/standardisation_profiles.nf +++ b/subworkflows/local/standardisation_profiles.nf @@ -3,11 +3,8 @@ // include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main' -include { - KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE; - KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_BRACKEN; - KRAKENTOOLS_COMBINEKREPORTS -} from '../../modules/nf-core/krakentools/combinekreports/main' +include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/krakentools/combinekreports/main' +include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main' include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main' include { MOTUS_MERGE } from '../../modules/nf-core/motus/merge/main' @@ -30,7 +27,6 @@ workflow STANDARDISATION_PROFILES { .branch { motus: it[0]['tool'] == 'motus' kraken2: it[0]['tool'] == 'kraken2' - bracken: it[0]['tool'] == 'bracken' centrifuge: it[0]['tool'] == 'centrifuge' metaphlan3: it[0]['tool'] == 'metaphlan3' unknown: true @@ -102,23 +98,6 @@ workflow STANDARDISATION_PROFILES { ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS.out.txt ) ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS.out.versions ) - // Bracken - - // Collect and replace id for db_name for prefix - // Have to sort by size to ensure first file actually has hits otherwise - // the script fails - ch_profiles_for_bracken = ch_input_profiles.bracken - .map { [it[0]['db_name'], it[1]] } - .groupTuple(sort: {-it.size()} ) - .map { - [[id:it[0]], it[1]] - } - - KRAKENTOOLS_COMBINEKREPORTS_BRACKEN ( ch_profiles_for_bracken ) - ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_BRACKEN.out.txt ) - ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_BRACKEN.out.txt ) - ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS_BRACKEN.out.versions ) - // MetaPhlAn3 ch_profiles_for_metaphlan3 = ch_input_profiles.metaphlan3