mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 15:49:55 +00:00
57 lines
1.5 KiB
Text
57 lines
1.5 KiB
Text
|
//
|
||
|
|
// Create Krona visualizations
|
||
|
|
//
|
||
|
|
|
||
|
|
include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main'
|
||
|
|
|
||
|
|
workflow STANDARDISATION_PROFILES {
|
||
|
|
take:
|
||
|
|
classifications
|
||
|
|
profiles
|
||
|
|
databases
|
||
|
|
motu_version
|
||
|
|
|
||
|
|
main:
|
||
|
|
ch_standardised_tables = Channel.empty()
|
||
|
|
ch_versions = Channel.empty()
|
||
|
|
|
||
|
|
/*
|
||
|
|
Split profile results based on tool they come from
|
||
|
|
*/
|
||
|
|
ch_input_profiles = profiles
|
||
|
|
.branch {
|
||
|
|
motus: it[0]['tool'] == 'motus'
|
||
|
|
unknown: true
|
||
|
|
}
|
||
|
|
|
||
|
|
ch_input_classifications = classifications
|
||
|
|
.branch {
|
||
|
|
unknown: true
|
||
|
|
}
|
||
|
|
|
||
|
|
ch_input_databases = databases
|
||
|
|
.branch {
|
||
|
|
motus: it[0]['tool'] == 'motus'
|
||
|
|
unknown: true
|
||
|
|
}
|
||
|
|
|
||
|
|
/*
|
||
|
|
Standardise and aggregate
|
||
|
|
*/
|
||
|
|
|
||
|
|
// mOTUs has a 'single' database, and cannot create custom ones.
|
||
|
|
// Therefore removing db info here, and publish merged at root mOTUs results
|
||
|
|
// directory
|
||
|
|
MOTUS_MERGE ( ch_input_profiles.motus.map{it[1]}.collect(), ch_input_databases.motus.map{it[1]}, motu_version, params.generate_biom_output )
|
||
|
|
if ( params.generate_biom_output ) {
|
||
|
|
ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.biom )
|
||
|
|
} else {
|
||
|
|
ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.txt )
|
||
|
|
}
|
||
|
|
ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions )
|
||
|
|
|
||
|
|
emit:
|
||
|
|
tables = ch_standardised_tables
|
||
|
|
versions = ch_versions
|
||
|
|
}
|