From a8a5172c90e48b28d45bf3fc904bcbeef859cec2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 31 May 2024 11:07:46 +0200 Subject: [PATCH 1/4] fix dbsnp usage --- workflows/rnavar/main.nf | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index bf06bb1..9fe15fb 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -253,8 +253,11 @@ workflow RNAVAR { interval_flag = params.no_intervals // Run haplotyper even in the absence of dbSNP files if (!params.dbsnp){ - ch_dbsnp = [] - ch_dbsnp_tbi = [] + ch_dbsnp_for_haplotypecaller = [[id:'null'], []] + ch_dbsnp_for_haplotypecaller_tbi = [[id:'null'], []] + } else { + ch_dbsnp_for_haplotypecaller = ch_dbsnp.map{ it -> [[id:it.baseName], it] }, + ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi.map{ it -> [[id:it.baseName], it] } } ch_haplotypecaller_vcf = Channel.empty() @@ -273,8 +276,8 @@ workflow RNAVAR { ch_fasta, ch_fasta_fai.map{ it -> [[id:it.baseName], it] }, ch_dict, - ch_dbsnp.map{ it -> [[id:it.baseName], it] }, - ch_dbsnp_tbi.map{ it -> [[id:it.baseName], it] } + ch_dbsnp_for_haplotypecaller, + ch_dbsnp_for_haplotypecaller_tbi ) ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf.map{ meta, vcf -> [ meta + [id:meta.sample] - meta.subMap('sample'), vcf ] }.groupTuple() From 74192bedeb7bd8d03643f8c8a7d814111433d980 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 31 May 2024 11:08:55 +0200 Subject: [PATCH 2/4] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a23056f..576a738 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#132](https://github.com/nf-core/rnavar/pull/132) - Added missing variantcaller key to meta map, to fix null value in publishDir - [#136](https://github.com/nf-core/rnavar/pull/136) - Replaced unzip module with gunzip, removed unzip module - [#138](https://github.com/nf-core/rnavar/pull/138) - Proper usage of GVCF +- [#142](https://github.com/nf-core/rnavar/pull/142) - Fix dbsnp channels ### Dependencies From 5be19815d5a6aaacc41deb353c28fe5bbd41ecfa Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 31 May 2024 14:13:54 +0200 Subject: [PATCH 3/4] fix dbsnp usage --- workflows/rnavar/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 9fe15fb..6b0a425 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -256,8 +256,8 @@ workflow RNAVAR { ch_dbsnp_for_haplotypecaller = [[id:'null'], []] ch_dbsnp_for_haplotypecaller_tbi = [[id:'null'], []] } else { - ch_dbsnp_for_haplotypecaller = ch_dbsnp.map{ it -> [[id:it.baseName], it] }, - ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi.map{ it -> [[id:it.baseName], it] } + ch_dbsnp_for_haplotypecaller = ch_dbsnp + ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi } ch_haplotypecaller_vcf = Channel.empty() From 358c6ffb3c250674d745fab11b98df3c231fe281 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 31 May 2024 16:08:53 +0200 Subject: [PATCH 4/4] fix dbsnp usage --- workflows/rnavar/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 6b0a425..ee77651 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -256,8 +256,8 @@ workflow RNAVAR { ch_dbsnp_for_haplotypecaller = [[id:'null'], []] ch_dbsnp_for_haplotypecaller_tbi = [[id:'null'], []] } else { - ch_dbsnp_for_haplotypecaller = ch_dbsnp - ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi + ch_dbsnp_for_haplotypecaller = ch_dbsnp.map{ vcf -> [[id:'dbsnp'], vcf] } + ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi.map{ tbi -> [[id:'dbsnp'], tbi] } } ch_haplotypecaller_vcf = Channel.empty()