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93 lines
3.3 KiB
Text
93 lines
3.3 KiB
Text
//
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// Standardise output files e.g. aggregation
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//
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include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
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include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main'
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include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/modules/metaphlan3/mergemetaphlantables/main'
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workflow STANDARDISATION_PROFILES {
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take:
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classifications
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profiles
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databases
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motu_version
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main:
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ch_standardised_tables = Channel.empty()
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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/*
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Split profile results based on tool they come from
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*/
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ch_input_profiles = profiles
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.branch {
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motus: it[0]['tool'] == 'motus'
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metaphlan3: it[0]['tool'] == 'metaphlan3'
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unknown: true
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}
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ch_input_classifications = classifications
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.branch {
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kaiju: it[0]['tool'] == 'kaiju'
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unknown: true
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}
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ch_input_databases = databases
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.branch {
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motus: it[0]['tool'] == 'motus'
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kaiju: it[0]['tool'] == 'kaiju'
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unknown: true
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}
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/*
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Standardise and aggregate
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*/
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// Kaiju
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// Collect and replace id for db_name for prefix
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ch_profiles_for_kaiju = ch_input_classifications.kaiju
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.map { [it[0]['db_name'], it[1]] }
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.groupTuple()
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.map {
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[[id:it[0]], it[1]]
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}
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KAIJU_KAIJU2TABLE ( ch_profiles_for_kaiju, ch_input_databases.kaiju.map{it[1]}, params.kaiju_taxon_rank)
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ch_standardised_tables = ch_standardised_tables.mix( KAIJU_KAIJU2TABLE.out.summary )
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
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ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
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// MetaPhlAn3
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ch_profiles_for_metaphlan3 = ch_input_profiles.metaphlan3
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.map { [it[0]['db_name'], it[1]] }
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.groupTuple()
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.map {
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[[id:it[0]], it[1]]
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}
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METAPHLAN3_MERGEMETAPHLANTABLES ( ch_profiles_for_metaphlan3 )
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ch_standardised_tables = ch_standardised_tables.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
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ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
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ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions )
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// mOTUs
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// mOTUs has a 'single' database, and cannot create custom ones.
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// Therefore removing db info here, and publish merged at root mOTUs results
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// directory
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MOTUS_MERGE ( ch_input_profiles.motus.map{it[1]}.collect(), ch_input_databases.motus.map{it[1]}, motu_version, params.generate_biom_output )
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if ( params.generate_biom_output ) {
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ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.biom )
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} else {
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ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.txt )
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}
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ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions )
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emit:
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tables = ch_standardised_tables
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versions = ch_versions
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mqc = ch_multiqc_files
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}
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