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Merge pull request #221 from nf-core/metaphlan3-filter-nanopore

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Filter  out nanopore data prior Metaphlan3
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James A. Fellows Yates 2023-01-24 14:39:02 +01:00 committed by GitHub
commit 00178d3431
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2 changed files with 4 additions and 3 deletions
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2
subworkflows/local/db_check.nf
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@ -40,7 +40,7 @@ workflow DB_CHECK {
} }
//Filter the channel to run untar on DBs of tools actually using //Filter the channel to run untar on DBs of tools actually using
ch_input_untar = ch_dbs_for_untar.untar.dump() ch_input_untar = ch_dbs_for_untar.untar
.filter { params.run_kraken2 && it[0]['tool'] == 'kraken2' || params.run_centrifuge && it[0]['tool'] == 'centrifuge' || params.run_bracken && it[0]['tool'] == 'bracken' || params.run_kaiju && it[0]['tool'] == 'kaiju' || params.run_krakenuniq && it [0]['tool'] == 'krakenuniq' || params.run_malt && it[0]['tool'] == 'malt' || params.run_metaphlan3 && it[0]['tool'] == 'metaphlan3' } .filter { params.run_kraken2 && it[0]['tool'] == 'kraken2' || params.run_centrifuge && it[0]['tool'] == 'centrifuge' || params.run_bracken && it[0]['tool'] == 'bracken' || params.run_kaiju && it[0]['tool'] == 'kaiju' || params.run_krakenuniq && it [0]['tool'] == 'krakenuniq' || params.run_malt && it[0]['tool'] == 'malt' || params.run_metaphlan3 && it[0]['tool'] == 'metaphlan3' }
UNTAR (ch_input_untar) UNTAR (ch_input_untar)
ch_versions = ch_versions.mix(UNTAR.out.versions.first()) ch_versions = ch_versions.mix(UNTAR.out.versions.first())

5
subworkflows/local/profiling.nf
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@ -203,6 +203,8 @@ workflow PROFILING {
.filter{ .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}." 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 !it[0].is_fasta
if (it[0].instrument_platform == 'OXFORD_NANOPORE') log.warn "[nf-core/taxprofiler] MetaPhlAn3 has not been evaluated for Nanopore data. Skipping MetaPhlAn3 for sample ${it[0].id}."
!it[0].instrument_platform == 'OXFORD_NANOPORE'
} }
.multiMap { .multiMap {
it -> it ->
@ -277,14 +279,13 @@ workflow PROFILING {
[[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db] [[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db]
} }
.groupTuple(by: [0,2,3]) .groupTuple(by: [0,2,3])
.dump(tag: "krakenuniq_premultimap")
.multiMap { .multiMap {
single_meta, reads, db_meta, db -> single_meta, reads, db_meta, db ->
reads: [ single_meta + db_meta, reads.flatten() ] reads: [ single_meta + db_meta, reads.flatten() ]
db: db db: db
} }
// Hardcode to _always_ produce the report file (which is our basic otput, and goes into) // Hardcode to _always_ produce the report file (which is our basic otput, and goes into)
KRAKENUNIQ_PRELOADEDKRAKENUNIQ ( ch_input_for_krakenuniq.reads.dump(tag: "krakenuniq_input"), ch_input_for_krakenuniq.db.dump(tag: "krakenuniq_db"), params.krakenuniq_ram_chunk_size, params.krakenuniq_save_reads, true, params.krakenuniq_save_readclassifications ) KRAKENUNIQ_PRELOADEDKRAKENUNIQ ( ch_input_for_krakenuniq.reads, ch_input_for_krakenuniq.db, params.krakenuniq_ram_chunk_size, params.krakenuniq_save_reads, true, params.krakenuniq_save_readclassifications )
ch_multiqc_files = ch_multiqc_files.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.report ) ch_multiqc_files = ch_multiqc_files.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.report )
ch_versions = ch_versions.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.versions.first() ) ch_versions = ch_versions.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.classified_assignment ) ch_raw_classifications = ch_raw_classifications.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.classified_assignment )