mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-23 21:49:56 +00:00
Try putting MillironX's krona in subworkflow
This commit is contained in:
James Fellows Yates
parent
0e44098125
commit
bb7323ef1d
4 changed files with 96 additions and 21 deletions
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@ -293,7 +293,16 @@ process {
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]
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}
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withName: KRONA_IMPORTKRAKEN {
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withName: KRAKENTOOLS_KREPORT2KRONA {
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: KRONA_KRAKENCLEANUP {
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: KRONA_KTIMPORTTEXT {
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ext.prefix = { "${meta.tool}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/krona" },
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mode: params.publish_dir_mode,
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66
subworkflows/local/postprocessing_krona.nf
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66
subworkflows/local/postprocessing_krona.nf
Normal file
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@ -0,0 +1,66 @@
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//
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// Remove host reads via alignment and export off-target reads
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//
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include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
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include { KRONA_CLEANUP as KRONA_KRAKENCLEANUP } from '../../modules/local/krona_cleanup'
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include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/modules/krona/ktimporttext/main'
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include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main'
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workflow POSTPROCESSING_KRONA {
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take:
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krona_input
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databases
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main:
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ch_versions = Channel.empty()
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ch_input_for_ktimporttext = Channel.empty()
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ch_files_for_krona = krona_input
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.branch {
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// malt:
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kraken2: it[0]['tool'] == 'kraken2'
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centrifuge: it[0]['tool'] == 'centrifuge'
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//metaphlan3:
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//kaiju:
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//diamond:
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}
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ch_databases = databases
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.branch{
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centrifuge: it[0]['tool'] == 'centrifuge'
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}
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// TODO PUSH BACK CENTRIFUGE_KREPORT TO PROFILING.NF WHERE DATABASE ALREADY IS?
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ch_input_for_centrifuge_kreport = ch_files_for_krona.centrifuge
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.dump(tag: "db_for_kreport_pre")
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.join(ch_databases, by: 0)
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.dump(tag: "db_for_kreport_post")
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// Kraken
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KRAKENTOOLS_KREPORT2KRONA ( ch_files_for_krona.kraken2 )
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KRONA_KRAKENCLEANUP ( KRAKENTOOLS_KREPORT2KRONA.out.txt )
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ch_kraken_for_krona = KRONA_KRAKENCLEANUP.out.txt
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.map{
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[[id: it[0].tool + "-" + it[0].db_name, db_name: it[0].db_name, tool: it[0].tool ], it[1]]
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}
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.groupTuple()
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ch_input_for_ktimporttext = ch_input_for_ktimporttext.mix( ch_kraken_for_krona )
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ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
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ch_versions = ch_versions.mix( KRONA_KRAKENCLEANUP.out.versions.first() )
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KRONA_KTIMPORTTEXT (ch_input_for_ktimporttext)
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ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
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// Centrifuge
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//CENTRIFUGE_KREPORT (krona_input.centrifuge, ch_input_for_centrifuge.db)
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// ch_versions = ch_versions.mix( /CENTRIFUGE_KREPORT.out.versions.first() )
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emit:
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versions = ch_versions // channel: [ versions.yml ]
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}
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@ -5,11 +5,7 @@
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include { MALT_RUN } from '../../modules/nf-core/modules/malt/run/main'
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include { MEGAN_RMA2INFO } from '../../modules/nf-core/modules/megan/rma2info/main'
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include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main'
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include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
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include { KRONA_CLEANUP as KRONA_KRAKENCLEANUP } from '../../modules/local/krona_cleanup'
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include { KRONA_KTIMPORTTEXT as KRONA_IMPORTKRAKEN } from '../../modules/nf-core/modules/krona/ktimporttext/main'
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include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
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include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main'
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include { METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/main'
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include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main'
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include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
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@ -24,8 +20,8 @@ workflow PROFILING {
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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ch_raw_profiles = Channel.empty()
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ch_visualizations = Channel.empty()
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ch_raw_profiles = Channel.empty()
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ch_output_for_krona = Channel.empty()
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/*
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COMBINE READS WITH POSSIBLE DATABASES
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@ -128,17 +124,11 @@ workflow PROFILING {
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}
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KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
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KRAKENTOOLS_KREPORT2KRONA ( KRAKEN2_KRAKEN2.out.report )
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KRONA_KRAKENCLEANUP ( KRAKENTOOLS_KREPORT2KRONA.out.txt )
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KRONA_IMPORTKRAKEN( KRONA_KRAKENCLEANUP.out.txt.map{[[id: it[0].db_name], it[1]]}.groupTuple() )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) )
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ch_visualizations = ch_visualizations.mix( KRONA_IMPORTKRAKEN.out.html )
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ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
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ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
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ch_versions = ch_versions.mix( KRONA_KRAKENCLEANUP.out.versions.first() )
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ch_versions = ch_versions.mix( KRONA_IMPORTKRAKEN.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) )
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ch_output_for_krona = ch_output_for_krona.mix( KRAKEN2_KRAKEN2.out.report )
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ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
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}
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@ -156,9 +146,11 @@ workflow PROFILING {
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}
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CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads )
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CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
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ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
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// TODO PUSH BACK CENTRIFUGE_KREPORT HERE WHERE DATABASE ALREADY IS?
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ch_output_for_krona = ch_output_for_krona.mix( CENTRIFUGE_CENTRIFUGE.out.report )
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ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_CENTRIFUGE.out.report )
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}
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@ -221,5 +213,5 @@ workflow PROFILING {
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profiles = ch_raw_profiles // channel: [ val(meta), [ reads ] ] - should be text files or biom
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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visualizations = ch_visualizations
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krona = ch_output_for_krona
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}
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@ -62,6 +62,7 @@ include { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_
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include { LONGREAD_HOSTREMOVAL } from '../subworkflows/local/longread_hostremoval'
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include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
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include { PROFILING } from '../subworkflows/local/profiling'
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include { POSTPROCESSING_KRONA } from '../subworkflows/local/postprocessing_krona'
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -209,6 +210,13 @@ workflow TAXPROFILER {
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PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
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ch_versions = ch_versions.mix( PROFILING.out.versions )
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/*
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SUBWORKFLOW: KRONA VISUALISATION
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*/
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POSTPROCESSING_KRONA ( PROFILING.out.krona, DB_CHECK.out.dbs )
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ch_versions = ch_versions.mix( POSTPROCESSING_KRONA.out.versions )
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/*
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MODULE: MultiQC
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*/
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