From c9a55b88db2da427e6daca84eb301ca455694e41 Mon Sep 17 00:00:00 2001 From: chasem Date: Wed, 21 Aug 2024 13:51:44 -0500 Subject: [PATCH 1/3] this adjusts the dbsnp channel mapping in variant_calling_germline_all to match variant_calling_sentieon_dnascope. null values are handled appropriately this way --- subworkflows/local/bam_variant_calling_germline_all/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/bam_variant_calling_germline_all/main.nf b/subworkflows/local/bam_variant_calling_germline_all/main.nf index 0065166bd9..deb15527d7 100644 --- a/subworkflows/local/bam_variant_calling_germline_all/main.nf +++ b/subworkflows/local/bam_variant_calling_germline_all/main.nf @@ -130,8 +130,8 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL { fasta, fasta_fai, dict, - dbsnp.map{ it -> [[id:it[0].baseName], it] }, - dbsnp_tbi.map{ it -> [[id:it[0].baseName], it] }, + dbsnp.map{it -> [[:], it]}, + dbsnp_tbi.map{it -> [[:], it]}, intervals) vcf_haplotypecaller = BAM_VARIANT_CALLING_HAPLOTYPECALLER.out.vcf From e654579e9c0ac542856a254097ced5c878700a8c Mon Sep 17 00:00:00 2001 From: chasem Date: Wed, 21 Aug 2024 13:57:36 -0500 Subject: [PATCH 2/3] updating changelog with 1628 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e786b51f10..7a36622743 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed - [1623](https://github.com/nf-core/sarek/pull/1623) - Update docs to clarify vep cache folder organisation +- [1628](https://github.com/nf-core/sarek/pull/1628) - fix dbsnp channel mapping in germline variant calling subworkflow ### Removed From e0cbf05a92859af0d3d49ff641ab8b0b463dd7dc Mon Sep 17 00:00:00 2001 From: Chase Mateusiak Date: Thu, 22 Aug 2024 13:06:44 -0500 Subject: [PATCH 3/3] fix type on 1628 entry in changelog Co-authored-by: Friederike Hanssen --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7a36622743..f27a1b7c9f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed - [1623](https://github.com/nf-core/sarek/pull/1623) - Update docs to clarify vep cache folder organisation -- [1628](https://github.com/nf-core/sarek/pull/1628) - fix dbsnp channel mapping in germline variant calling subworkflow +- [1628](https://github.com/nf-core/sarek/pull/1628) - Fix dbsnp channel mapping in germline variant calling subworkflow ### Removed