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
|
|
@ -293,7 +293,16 @@ process {
|
|||
]
|
||||
}
|
||||
|
||||
withName: KRONA_IMPORTKRAKEN {
|
||||
withName: KRAKENTOOLS_KREPORT2KRONA {
|
||||
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
||||
}
|
||||
|
||||
withName: KRONA_KRAKENCLEANUP {
|
||||
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
||||
}
|
||||
|
||||
withName: KRONA_KTIMPORTTEXT {
|
||||
ext.prefix = { "${meta.tool}-${meta.db_name}" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/krona" },
|
||||
mode: params.publish_dir_mode,
|
||||
|
|
|
|||
66
subworkflows/local/postprocessing_krona.nf
Normal file
66
subworkflows/local/postprocessing_krona.nf
Normal file
|
|
@ -0,0 +1,66 @@
|
|||
//
|
||||
// Remove host reads via alignment and export off-target reads
|
||||
//
|
||||
|
||||
include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
|
||||
include { KRONA_CLEANUP as KRONA_KRAKENCLEANUP } from '../../modules/local/krona_cleanup'
|
||||
include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/modules/krona/ktimporttext/main'
|
||||
include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main'
|
||||
|
||||
workflow POSTPROCESSING_KRONA {
|
||||
take:
|
||||
krona_input
|
||||
databases
|
||||
|
||||
main:
|
||||
ch_versions = Channel.empty()
|
||||
ch_input_for_ktimporttext = Channel.empty()
|
||||
|
||||
ch_files_for_krona = krona_input
|
||||
.branch {
|
||||
// malt:
|
||||
kraken2: it[0]['tool'] == 'kraken2'
|
||||
centrifuge: it[0]['tool'] == 'centrifuge'
|
||||
//metaphlan3:
|
||||
//kaiju:
|
||||
//diamond:
|
||||
}
|
||||
|
||||
ch_databases = databases
|
||||
.branch{
|
||||
centrifuge: it[0]['tool'] == 'centrifuge'
|
||||
}
|
||||
|
||||
// TODO PUSH BACK CENTRIFUGE_KREPORT TO PROFILING.NF WHERE DATABASE ALREADY IS?
|
||||
ch_input_for_centrifuge_kreport = ch_files_for_krona.centrifuge
|
||||
.dump(tag: "db_for_kreport_pre")
|
||||
.join(ch_databases, by: 0)
|
||||
.dump(tag: "db_for_kreport_post")
|
||||
|
||||
|
||||
// Kraken
|
||||
KRAKENTOOLS_KREPORT2KRONA ( ch_files_for_krona.kraken2 )
|
||||
KRONA_KRAKENCLEANUP ( KRAKENTOOLS_KREPORT2KRONA.out.txt )
|
||||
ch_kraken_for_krona = KRONA_KRAKENCLEANUP.out.txt
|
||||
.map{
|
||||
[[id: it[0].tool + "-" + it[0].db_name, db_name: it[0].db_name, tool: it[0].tool ], it[1]]
|
||||
}
|
||||
.groupTuple()
|
||||
ch_input_for_ktimporttext = ch_input_for_ktimporttext.mix( ch_kraken_for_krona )
|
||||
ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
|
||||
ch_versions = ch_versions.mix( KRONA_KRAKENCLEANUP.out.versions.first() )
|
||||
|
||||
|
||||
KRONA_KTIMPORTTEXT (ch_input_for_ktimporttext)
|
||||
|
||||
|
||||
ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
|
||||
|
||||
// Centrifuge
|
||||
//CENTRIFUGE_KREPORT (krona_input.centrifuge, ch_input_for_centrifuge.db)
|
||||
// ch_versions = ch_versions.mix( /CENTRIFUGE_KREPORT.out.versions.first() )
|
||||
|
||||
emit:
|
||||
versions = ch_versions // channel: [ versions.yml ]
|
||||
}
|
||||
|
||||
|
|
@ -5,11 +5,7 @@
|
|||
include { MALT_RUN } from '../../modules/nf-core/modules/malt/run/main'
|
||||
include { MEGAN_RMA2INFO } from '../../modules/nf-core/modules/megan/rma2info/main'
|
||||
include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main'
|
||||
include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
|
||||
include { KRONA_CLEANUP as KRONA_KRAKENCLEANUP } from '../../modules/local/krona_cleanup'
|
||||
include { KRONA_KTIMPORTTEXT as KRONA_IMPORTKRAKEN } from '../../modules/nf-core/modules/krona/ktimporttext/main'
|
||||
include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
|
||||
include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/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'
|
||||
|
|
@ -25,7 +21,7 @@ workflow PROFILING {
|
|||
ch_versions = Channel.empty()
|
||||
ch_multiqc_files = Channel.empty()
|
||||
ch_raw_profiles = Channel.empty()
|
||||
ch_visualizations = Channel.empty()
|
||||
ch_output_for_krona = Channel.empty()
|
||||
|
||||
/*
|
||||
COMBINE READS WITH POSSIBLE DATABASES
|
||||
|
|
@ -128,16 +124,10 @@ workflow PROFILING {
|
|||
}
|
||||
|
||||
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_visualizations = ch_visualizations.mix( KRONA_IMPORTKRAKEN.out.html )
|
||||
ch_output_for_krona = ch_output_for_krona.mix( KRAKEN2_KRAKEN2.out.report )
|
||||
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 )
|
||||
|
||||
}
|
||||
|
|
@ -156,9 +146,11 @@ workflow PROFILING {
|
|||
}
|
||||
|
||||
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads )
|
||||
CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
|
||||
// TODO PUSH BACK CENTRIFUGE_KREPORT HERE WHERE DATABASE ALREADY IS?
|
||||
|
||||
ch_output_for_krona = ch_output_for_krona.mix( CENTRIFUGE_CENTRIFUGE.out.report )
|
||||
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_CENTRIFUGE.out.report )
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -221,5 +213,5 @@ workflow PROFILING {
|
|||
profiles = ch_raw_profiles // channel: [ val(meta), [ reads ] ] - should be text files or biom
|
||||
versions = ch_versions // channel: [ versions.yml ]
|
||||
mqc = ch_multiqc_files
|
||||
visualizations = ch_visualizations
|
||||
krona = ch_output_for_krona
|
||||
}
|
||||
|
|
|
|||
|
|
@ -62,6 +62,7 @@ include { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_
|
|||
include { LONGREAD_HOSTREMOVAL } from '../subworkflows/local/longread_hostremoval'
|
||||
include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
|
||||
include { PROFILING } from '../subworkflows/local/profiling'
|
||||
include { POSTPROCESSING_KRONA } from '../subworkflows/local/postprocessing_krona'
|
||||
|
||||
/*
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
|
@ -209,6 +210,13 @@ workflow TAXPROFILER {
|
|||
PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
|
||||
ch_versions = ch_versions.mix( PROFILING.out.versions )
|
||||
|
||||
/*
|
||||
SUBWORKFLOW: KRONA VISUALISATION
|
||||
*/
|
||||
POSTPROCESSING_KRONA ( PROFILING.out.krona, DB_CHECK.out.dbs )
|
||||
ch_versions = ch_versions.mix( POSTPROCESSING_KRONA.out.versions )
|
||||
|
||||
|
||||
/*
|
||||
MODULE: MultiQC
|
||||
*/
|
||||
|
|
|
|||
Loading…
Reference in a new issue