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taxprofiler/subworkflows/local/profiling.nf
James Fellows Yates 030099c559 A bit of clean up
2022-04-10 07:26:20 +02:00

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//
// Run profiling
//
include { MALT_RUN } from '../../modules/nf-core/modules/malt/run/main'
include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main'
include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
include { METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/main'
workflow PROFILING {
take:
shortreads // [ [ meta ], [ reads ] ]
longreads // [ [ meta ], [ reads ] ]
databases // [ [ meta ], path ]
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
/*
COMBINE READS WITH POSSIBLE DATABASES
*/
// e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
ch_input_for_profiling = shortreads
.mix( longreads )
.combine(databases)
.branch {
malt: it[2]['tool'] == 'malt'
kraken2: it[2]['tool'] == 'kraken2'
metaphlan3: it[2]['tool'] == 'metaphlan3'
centrifuge: it[2]['tool'] == 'centrifuge'
unknown: true
}
/*
PREPARE PROFILER INPUT CHANNELS
*/
// Each tool as a slightly different input structure and generally separate
// input channels for reads vs databases. We restructure the channel tuple
// for each tool and make liberal use of multiMap to keep reads/databases
// channel element order in sync with each other
// MALT: We groupTuple to have all samples in one channel for MALT as database
// loading takes a long time, so we only want to run it once per database
// TODO document somewhere we only accept illumina short reads for MALT?
ch_input_for_malt = ch_input_for_profiling.malt
.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
.map {
it ->
def temp_meta = [ id: it[2]['db_name']] + it[2]
def db = it[3]
[ temp_meta, it[1], db ]
}
.groupTuple(by: [0,2])
.multiMap {
it ->
reads: [ it[0], it[1].flatten() ]
db: it[2]
}
// All subsequent tools can easily run on a per-sample basis
ch_input_for_kraken2 = ch_input_for_profiling.kraken2
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
db: it[3]
}
ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
db: it[3]
}
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.multiMap {
it ->
reads: [it[0] + it[2], it[1]]
db: it[3]
}
/*
RUN PROFILING
*/
if ( params.run_malt ) {
MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() )
}
if ( params.run_kraken2 ) {
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
}
if ( params.run_centrifuge ) {
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_unaligned, params.centrifuge_save_aligned, params.centrifuge_sam_format )
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
}
if ( params.run_metaphlan3 ) {
METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
ch_versions = ch_versions.mix( METAPHLAN3.out.versions.first() )
}
emit:
// TODO work out if there is enough standardisation of output to export as one?
//output = ch_filtered_reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}