diff --git a/subworkflows/local/db_check.nf b/subworkflows/local/db_check.nf index a89b519..96ae7a1 100644 --- a/subworkflows/local/db_check.nf +++ b/subworkflows/local/db_check.nf @@ -40,7 +40,7 @@ workflow DB_CHECK { } //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' } UNTAR (ch_input_untar) ch_versions = ch_versions.mix(UNTAR.out.versions.first()) diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index f6eddb0..accab37 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -202,8 +202,10 @@ workflow PROFILING { ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3 .filter{ - if (it[0].is_fasta || it[0].instrument_platform == 'OXFORD_NANOPORE' ) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input and/or has not been evaluated for Nanopore data. Skipping MetaPhlAn3 for sample ${it[0].id}." - !(it[0].is_fasta || it[0].instrument_platform == 'OXFORD_NANOPORE') + 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 + 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 { it -> @@ -278,14 +280,13 @@ workflow PROFILING { [[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db] } .groupTuple(by: [0,2,3]) - .dump(tag: "krakenuniq_premultimap") .multiMap { single_meta, reads, db_meta, db -> reads: [ single_meta + db_meta, reads.flatten() ] db: db } // 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_versions = ch_versions.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.versions.first() ) ch_raw_classifications = ch_raw_classifications.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.classified_assignment )