From 6307a9cf4342a05fdc6cb2a127527a66d3993155 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Mon, 18 Apr 2022 07:28:09 +0200 Subject: [PATCH] Typos --- subworkflows/local/profiling.nf | 2 +- workflows/taxprofiler.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index f2f7eb7..156259b 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -76,7 +76,7 @@ workflow PROFILING { ch_input_for_centrifuge = ch_input_for_profiling.centrifuge .filter{ - if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge does not accept FASTA files as input. Skipping Centrifuge for sample " + it[0].id + if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample " + it[0].id !it[0].is_fasta } .multiMap { diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index e7ff78b..884ee46 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -19,7 +19,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true // Check mandatory parameters if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' } -if (params.shortread_clipmerge_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_clipmerge_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_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs" if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }