From d48b3be5a780d87b30c8f9ce189a062676cc601a Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 3 Jun 2022 13:55:17 +0200 Subject: [PATCH] Tweak DIAMOND save_reads message --- nextflow.config | 2 +- workflows/taxprofiler.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 11cbfc0..e5b8a1d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -124,7 +124,7 @@ params { // diamond run_diamond = false diamond_output_format = 'tsv' // TSV is only format with taxonomic information apparently - diamond_save_reads = false // this will override diamound output format so no taxonomic profile is generated! + diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated! } // Load base.config by default for all pipelines diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index 6a05dbe..f29a366 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -33,7 +33,7 @@ if (params.hostremoval_reference ) { ch_reference = file(params.hostre if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = file(params.shortread_hostremoval_index ) } else { ch_shortread_reference_index = [] } if (params.longread_hostremoval_index ) { ch_longread_reference_index = file(params.longread_hostremoval_index ) } else { ch_longread_reference_index = [] } -if (params.diamond_save_reads ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. Only aligned reads in SAM format will be produced, no taxonomic profiles will be available." +if (params.diamond_save_reads ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. As --diamond_save_reads supplied, only aligned reads in SAM format will be produced, no taxonomic profiles will be available." /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~