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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
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@ -48,7 +48,7 @@ workflow PROFILING {
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}
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}
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/*
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/*
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PREPARE PROFILER INPUT CHANNELS
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PREPARE PROFILER INPUT CHANNELS & RUN PROFILING
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*/
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*/
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// Each tool as a slightly different input structure and generally separate
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// Each tool as a slightly different input structure and generally separate
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@ -56,74 +56,27 @@ workflow PROFILING {
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// for each tool and make liberal use of multiMap to keep reads/databases
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// for each tool and make liberal use of multiMap to keep reads/databases
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// channel element order in sync with each other
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// channel element order in sync with each other
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// MALT: We groupTuple to have all samples in one channel for MALT as database
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// loading takes a long time, so we only want to run it once per database
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// TODO document somewhere we only accept illumina short reads for MALT?
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ch_input_for_malt = ch_input_for_profiling.malt
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.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
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.map {
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it ->
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def temp_meta = [ id: it[2]['db_name']] + it[2]
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def db = it[3]
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[ temp_meta, it[1], db ]
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}
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.groupTuple(by: [0,2])
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.multiMap {
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it ->
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reads: [ it[0], it[1].flatten() ]
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db: it[2]
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}
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// All subsequent tools can easily run on a per-sample basis
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ch_input_for_kraken2 = ch_input_for_profiling.kraken2
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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db: it[3]
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}
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ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
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.filter{
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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}."
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!it[0].is_fasta
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}
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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db: it[3]
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}
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ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
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.filter{
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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}."
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!it[0].is_fasta
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}
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.multiMap {
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it ->
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reads: [it[0] + it[2], it[1]]
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db: it[3]
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}
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ch_input_for_kaiju = ch_input_for_profiling.kaiju
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.multiMap {
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it ->
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reads: [it[0] + it[2], it[1]]
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db: it[3]
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}
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ch_input_for_diamond = ch_input_for_profiling.diamond
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.multiMap {
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it ->
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reads: [it[0] + it[2], it[1]]
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db: it[3]
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}
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/*
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RUN PROFILING
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*/
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if ( params.run_malt ) {
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if ( params.run_malt ) {
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// MALT: We groupTuple to have all samples in one channel for MALT as database
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// loading takes a long time, so we only want to run it once per database
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// TODO document somewhere we only accept illumina short reads for MALT?
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ch_input_for_malt = ch_input_for_profiling.malt
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.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
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.map {
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it ->
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def temp_meta = [ id: it[2]['db_name']] + it[2]
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def db = it[3]
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[ temp_meta, it[1], db ]
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}
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.groupTuple(by: [0,2])
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.multiMap {
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it ->
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reads: [ it[0], it[1].flatten() ]
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db: it[2]
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}
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MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
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MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
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ch_maltrun_for_megan = MALT_RUN.out.rma6
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ch_maltrun_for_megan = MALT_RUN.out.rma6
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@ -143,40 +96,94 @@ workflow PROFILING {
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ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
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ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
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ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
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ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
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}
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}
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if ( params.run_kraken2 ) {
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if ( params.run_kraken2 ) {
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ch_input_for_kraken2 = ch_input_for_profiling.kraken2
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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db: it[3]
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}
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KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
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KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
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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.txt )
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ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.txt )
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}
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}
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if ( params.run_centrifuge ) {
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if ( params.run_centrifuge ) {
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ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
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.filter{
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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}."
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!it[0].is_fasta
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}
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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db: it[3]
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}
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CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_unaligned, params.centrifuge_save_aligned, params.centrifuge_sam_format )
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CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_unaligned, params.centrifuge_save_aligned, params.centrifuge_sam_format )
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CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
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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_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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ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
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}
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}
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if ( params.run_metaphlan3 ) {
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if ( params.run_metaphlan3 ) {
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ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
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.filter{
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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}."
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!it[0].is_fasta
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}
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.multiMap {
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it ->
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reads: [it[0] + it[2], it[1]]
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db: it[3]
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}
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METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
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METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
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ch_versions = ch_versions.mix( METAPHLAN3.out.versions.first() )
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ch_versions = ch_versions.mix( METAPHLAN3.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( METAPHLAN3.out.biom )
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ch_raw_profiles = ch_raw_profiles.mix( METAPHLAN3.out.biom )
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}
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}
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if ( params.run_kaiju ) {
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if ( params.run_kaiju ) {
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ch_input_for_kaiju = ch_input_for_profiling.kaiju
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.multiMap {
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it ->
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reads: [it[0] + it[2], it[1]]
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db: it[3]
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}
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KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
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KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
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KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
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KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary.collect{it[1]}.ifEmpty([]) )
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
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ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
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ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
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}
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}
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if ( params.run_diamond ) {
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if ( params.run_diamond ) {
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ch_input_for_diamond = ch_input_for_profiling.diamond
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.multiMap {
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it ->
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reads: [it[0] + it[2], it[1]]
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db: it[3]
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}
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DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, params.diamond_output_format )
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DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, params.diamond_output_format )
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ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
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ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.output )
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ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.output )
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}
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}
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emit:
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emit:
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