From 0358489be0f4098b1f2cee1a9c396f5a37cd08e3 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 24 Jan 2023 13:05:52 +0100 Subject: [PATCH] Remove metaphlan profiling for nanopore as it appears to always result in 100% unclassified --- subworkflows/local/profiling.nf | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index 38936eb..f6eddb0 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -202,11 +202,8 @@ workflow PROFILING { ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3 .filter{ - meta, report -> - if (meta.is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input. Skipping MetaPhlAn3 for sample ${meta.id}." - !meta.is_fasta - if ( meta['instrument_platform'] == 'OXFORD_NANOPORE' ) log.warn "[nf-core/taxprofiler] MetaPhlAn3 has not been evaluated for Nanopore data. Skipping MetaPhlAn3 for sample ${meta.id}." - meta['tool'] == 'metaphlan3' && meta['instrument_platform'] != 'OXFORD_NANOPORE' + 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') } .multiMap { it ->