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Create VISUALIZATION_KRONA workflow to create Krona charts

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Thomas A. Christensen II 2022-06-27 08:22:47 -05:00
parent 5da8d5b741
commit a40a442178
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 55 additions and 0 deletions
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subworkflows/local/visualization_krona.nf Normal file
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//
// Create Krona visualizations
//
include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
include { KRONA_CLEANUP } from '../../modules/local/krona_cleanup'
include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/modules/krona/ktimporttext/main'
workflow VISUALIZATION_KRONA {
take:
profiles
main:
ch_krona_text = Channel.empty()
ch_krona_html = Channel.empty()
ch_versions = Channel.empty()
/*
Split profile results based on tool they come from
*/
ch_input_profiles = profiles
.branch {
kraken2: it[0]['tool'] == 'kraken2'
unknown: true
}
/*
Convert Kraken2 formatted reports into Krona text files
*/
ch_kraken_reports = ch_input_profiles.kraken2
KRAKENTOOLS_KREPORT2KRONA ( ch_kraken_reports )
ch_krona_text = ch_krona_text.mix( KRAKENTOOLS_KREPORT2KRONA.out.txt )
ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
/*
Remove taxonomy level annotations from the Krona text files
*/
KRONA_CLEANUP( ch_krona_text )
ch_cleaned_krona_text = KRONA_CLEANUP.out.txt
ch_versions = ch_versions.mix( KRONA_CLEANUP.out.versions.first() )
/*
Convert Krona text files into html Krona visualizations
*/
ch_krona_text_for_import = ch_cleaned_krona_text
.map{[[id: it[0]['db_name']], it[1]]}
.groupTuple()
KRONA_KTIMPORTTEXT( ch_krona_text_for_import )
ch_krona_html = ch_krona_html.mix( KRONA_KTIMPORTTEXT.out.html )
ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
emit:
html = ch_krona_html
versions = ch_versions
}