mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 10:49:55 +00:00
Merge pull request #75 from nf-core/improve-error-message
Only create profiler input channels when profiler activated
This commit is contained in:
James A. Fellows Yates
GitHub
commit
e7b54801ed
1 changed files with 75 additions and 68 deletions
|
|
@ -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 +56,27 @@ 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 +96,94 @@ 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:
|
||||
|
|
|
|||
Loading…
Reference in a new issue