From 589048edd25a582850fbf9148b174926016abe39 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Fri, 16 Oct 2020 10:20:27 +0200 Subject: [PATCH 1/2] fix: typo CamelCase -> snake_case --- main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index 27cca67e74..641db74cd4 100644 --- a/main.nf +++ b/main.nf @@ -214,8 +214,8 @@ skipQC = params.skip_qc ? params.skip_qc == 'all' ? skipQClist : params.skip_qc. if (!checkParameterList(skipQC, skipQClist)) exit 1, 'Unknown QC tool(s), see --help for more information' annoList = defineAnnoList() -annotateTools = params.annotate_tools ? params.annotate_tools.split(',').collect{it.trim().toLowerCase().replaceAll('-', '')} : [] -if (!checkParameterList(annotateTools,annoList)) exit 1, 'Unknown tool(s) to annotate, see --help for more information' +annotate_tools = params.annotate_tools ? params.annotate_tools.split(',').collect{it.trim().toLowerCase().replaceAll('-', '')} : [] +if (!checkParameterList(annotate_tools,annoList)) exit 1, 'Unknown tool(s) to annotate, see --help for more information' // Check parameters if ((params.ascat_ploidy && !params.ascat_purity) || (!params.ascat_ploidy && params.ascat_purity)) exit 1, 'Please specify both --ascat_purity and --ascat_ploidy, or none of them' @@ -3500,9 +3500,9 @@ if (step == 'annotate') { Channel.fromPath("${params.outdir}/VariantCalling/*/TIDDIT/*.vcf.gz") .flatten().map{vcf -> ['TIDDIT', vcf.minus(vcf.fileName)[-2].toString(), vcf]} ).choice(vcfToAnnotate, vcfNoAnnotate) { - annotateTools == [] || (annotateTools != [] && it[0] in annotateTools) ? 0 : 1 + annotate_tools == [] || (annotate_tools != [] && it[0] in annotate_tools) ? 0 : 1 } - } else if (annotateTools == []) { + } else if (annotate_tools == []) { // Annotate user-submitted VCFs // If user-submitted, Sarek assume that the idSample should be assumed automatically vcfToAnnotate = Channel.fromPath(tsvPath) From 29d66a5555eb55036af76d22856aed5dc1ea4384 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Fri, 16 Oct 2020 10:21:42 +0200 Subject: [PATCH 2/2] chores: update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d7a903deb6..f1ac507321 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,6 +29,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) - [#272](https://github.com/nf-core/sarek/pull/272) - Fix annotation `--tools merge` issue - [#279](https://github.com/nf-core/sarek/pull/279) - Fix issue with `--step prepare_recalibration` [#267](https://github.com/nf-core/sarek/issues/267) - [#280](https://github.com/nf-core/sarek/pull/280) - Use HTML codes instead of `<` and `>` in docs +- [#293](https://github.com/nf-core/sarek/pull/293) - Fix typo issue when printing infos [#292](https://github.com/nf-core/sarek/issues/292) ### Removed