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Only create profiler input channels when profiler activate

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James Fellows Yates 2022-05-01 07:24:58 +02:00
parent 2bae9d58ee
commit 4094706421
1 changed files with 74 additions and 68 deletions
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142
subworkflows/local/profiling.nf
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@ -48,7 +48,7 @@ workflow PROFILING {
}
/*
PREPARE PROFILER INPUT CHANNELS
PREPARE PROFILER INPUT CHANNELS & RUN PROFILING
*/
// Each tool as a slightly different input structure and generally separate
@ -56,74 +56,26 @@ workflow PROFILING {
// 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
.filter{
if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample ${it[0].id}."
!it[0].is_fasta
}
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
db: it[3]
}
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.filter{
if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input. Skipping MetaPhlAn3 for sample ${it[0].id}."
!it[0].is_fasta
}
.multiMap {
it ->
reads: [it[0] + it[2], it[1]]
db: it[3]
}
ch_input_for_kaiju = ch_input_for_profiling.kaiju
.multiMap {
it ->
reads: [it[0] + it[2], it[1]]
db: it[3]
}
ch_input_for_diamond = ch_input_for_profiling.diamond
.multiMap {
it ->
reads: [it[0] + it[2], it[1]]
db: it[3]
}
/*
RUN PROFILING
*/
if ( params.run_malt ) {
// 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]
MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
ch_maltrun_for_megan = MALT_RUN.out.rma6
@ -143,40 +95,94 @@ workflow PROFILING {
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(), MEGAN_RMA2INFO.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
}
if ( params.run_kraken2 ) {
ch_input_for_kraken2 = ch_input_for_profiling.kraken2
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
db: it[3]
}
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() )
ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.txt )
}
if ( params.run_centrifuge ) {
ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
.filter{
if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample ${it[0].id}."
!it[0].is_fasta
}
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
db: it[3]
}
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_unaligned, params.centrifuge_save_aligned, params.centrifuge_sam_format )
CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
}
if ( params.run_metaphlan3 ) {
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.filter{
if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input. Skipping MetaPhlAn3 for sample ${it[0].id}."
!it[0].is_fasta
}
.multiMap {
it ->
reads: [it[0] + it[2], it[1]]
db: it[3]
}
METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
ch_versions = ch_versions.mix( METAPHLAN3.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( METAPHLAN3.out.biom )
}
if ( params.run_kaiju ) {
ch_input_for_kaiju = ch_input_for_profiling.kaiju
.multiMap {
it ->
reads: [it[0] + it[2], it[1]]
db: it[3]
}
KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
}
if ( params.run_diamond ) {
ch_input_for_diamond = ch_input_for_profiling.diamond
.multiMap {
it ->
reads: [it[0] + it[2], it[1]]
db: it[3]
}
DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, params.diamond_output_format )
ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.output )
}
emit: