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Add Krona creation and formatting to PROFILING subworkflow

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Thomas A. Christensen II 2022-06-14 08:48:01 -05:00
parent 5da8d5b741
commit fa87975983
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 21 additions and 10 deletions
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31
subworkflows/local/profiling.nf
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@ -2,15 +2,18 @@
// Run profiling // Run profiling
// //
include { MALT_RUN } from '../../modules/nf-core/modules/malt/run/main' include { MALT_RUN } from '../../modules/nf-core/modules/malt/run/main'
include { MEGAN_RMA2INFO } from '../../modules/nf-core/modules/megan/rma2info/main' include { MEGAN_RMA2INFO } from '../../modules/nf-core/modules/megan/rma2info/main'
include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main' include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main'
include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main' include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main' include { KRONA_CLEANUP as KRONA_KRAKENCLEANUP } from '../../modules/local/krona_cleanup'
include { METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/main' include { KRONA_KTIMPORTTEXT as KRONA_IMPORTKRAKEN } from '../../modules/nf-core/modules/krona/ktimporttext/main'
include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main' include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main' include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/modules/diamond/blastx/main' include { METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/main'
include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main'
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/modules/diamond/blastx/main'
workflow PROFILING { workflow PROFILING {
@ -22,6 +25,7 @@ workflow PROFILING {
ch_versions = Channel.empty() ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty() ch_multiqc_files = Channel.empty()
ch_raw_profiles = Channel.empty() ch_raw_profiles = Channel.empty()
ch_visualizations = Channel.empty()
/* /*
COMBINE READS WITH POSSIBLE DATABASES COMBINE READS WITH POSSIBLE DATABASES
@ -124,8 +128,16 @@ workflow PROFILING {
} }
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification ) KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
KRAKENTOOLS_KREPORT2KRONA ( KRAKEN2_KRAKEN2.out.report )
KRONA_KRAKENCLEANUP ( KRAKENTOOLS_KREPORT2KRONA.out.txt )
KRONA_IMPORTKRAKEN( KRONA_KRAKENCLEANUP.out.txt.map{[[id: it[0].db_name], it[1]]}.groupTuple() )
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) ) ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) )
ch_visualizations = ch_visualizations.mix( KRONA_IMPORTKRAKEN.out.html )
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() ) ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
ch_versions = ch_versions.mix( KRONA_KRAKENCLEANUP.out.versions.first() )
ch_versions = ch_versions.mix( KRONA_IMPORTKRAKEN.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report ) ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
} }
@ -210,4 +222,3 @@ workflow PROFILING {
versions = ch_versions // channel: [ versions.yml ] versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files mqc = ch_multiqc_files
} }