From 0809a4083e7f7e28ff2476a639f7bd0f73aa46ce Mon Sep 17 00:00:00 2001 From: Alexander Koc Date: Thu, 11 Jan 2024 09:33:57 +0100 Subject: [PATCH 1/2] Change hardcoded platform value to params.platform --- conf/modules/align_MT.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules/align_MT.config b/conf/modules/align_MT.config index 23ab1c8c..2dcacdef 100644 --- a/conf/modules/align_MT.config +++ b/conf/modules/align_MT.config @@ -42,7 +42,7 @@ process { ext.args = { [ "--VALIDATION_STRINGENCY LENIENT", "--RGLB lib", - "--RGPL ILLUMINA", + "--RGPL ${params.platform}", "--RGPU barcode", "--RGSM ${meta.id}" ].join(' ').trim() } From a8b62e9a4c251a31797926ebda3bafedc445df48 Mon Sep 17 00:00:00 2001 From: Alexander Koc Date: Thu, 11 Jan 2024 10:47:07 +0100 Subject: [PATCH 2/2] Update Changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index da62b9db..3f7e0d50 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -37,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Replaced the parameter skip_mt_analysis which was used to turn on/off the mitochondrial workflow [#419](https://github.com/nf-core/raredisease/pull/419) - Adds a new parameter skip_mt_annotation which can be used to turn on/off annotation and ranking for mitochondrial SNVs [#419](https://github.com/nf-core/raredisease/pull/419) - Changed the name of the parameter from `skip_cnv_calling` to `skip_germlinecnvcaller` [#435](https://github.com/nf-core/raredisease/pull/435) +- Change hardcoded platform value to params.platform in align_MT.config [#475](https://github.com/nf-core/raredisease/pull/475) ### `Fixed`