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refactor: create standardized Bracken reports

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This commit is contained in:
Moritz E. Beber 2022-10-17 17:33:24 +02:00
parent fd8a0df2a6
commit 48b00b7d62
1 changed files with 23 additions and 2 deletions
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25
subworkflows/local/standardisation_profiles.nf
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@ -3,8 +3,11 @@
// //
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main' include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/krakentools/combinekreports/main' include {
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main' KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE;
KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_BRACKEN;
KRAKENTOOLS_COMBINEKREPORTS
} from '../../modules/nf-core/krakentools/combinekreports/main'
include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main' include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main'
include { MOTUS_MERGE } from '../../modules/nf-core/motus/merge/main' include { MOTUS_MERGE } from '../../modules/nf-core/motus/merge/main'
@ -27,6 +30,7 @@ workflow STANDARDISATION_PROFILES {
.branch { .branch {
motus: it[0]['tool'] == 'motus' motus: it[0]['tool'] == 'motus'
kraken2: it[0]['tool'] == 'kraken2' kraken2: it[0]['tool'] == 'kraken2'
bracken: it[0]['tool'] == 'bracken'
centrifuge: it[0]['tool'] == 'centrifuge' centrifuge: it[0]['tool'] == 'centrifuge'
metaphlan3: it[0]['tool'] == 'metaphlan3' metaphlan3: it[0]['tool'] == 'metaphlan3'
unknown: true unknown: true
@ -98,6 +102,23 @@ workflow STANDARDISATION_PROFILES {
ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS.out.txt ) ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS.out.txt )
ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS.out.versions ) 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 // MetaPhlAn3
ch_profiles_for_metaphlan3 = ch_input_profiles.metaphlan3 ch_profiles_for_metaphlan3 = ch_input_profiles.metaphlan3