From cac6f54d2d67b64e23e591813678f052afe20406 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 20 Jan 2023 13:36:17 +0100 Subject: [PATCH] [extra] Fix warn related to recently changed parameter --- workflows/taxprofiler.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index d1693be..7a09573 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -29,7 +29,7 @@ if ( params.input ) { if (params.databases) { ch_databases = file(params.databases, checkIfExists: true) } else { exit 1, 'Input database sheet not specified!' } -if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files." +if (!params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files." if (params.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging is not turned on. Please specify --shortread_qc_mergepairs" if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' )) exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_qc and/or --shortread_qc_tool 'fastp'"