From cb090b222882901326876431ce4e9b1da7488806 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 2 Jun 2023 16:38:59 +0200 Subject: [PATCH 1/3] fix comment --- subworkflows/local/bam_variant_calling_single_strelka/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/bam_variant_calling_single_strelka/main.nf b/subworkflows/local/bam_variant_calling_single_strelka/main.nf index 233bc0dbef..1d3e34d81b 100644 --- a/subworkflows/local/bam_variant_calling_single_strelka/main.nf +++ b/subworkflows/local/bam_variant_calling_single_strelka/main.nf @@ -42,7 +42,7 @@ workflow BAM_VARIANT_CALLING_SINGLE_STRELKA { MERGE_STRELKA_GENOME(genome_vcf_to_merge, dict) // Mix intervals and no_intervals channels together - // Only strelka variant vcf SV should get annotated + // Only strelka variant vcf should get annotated vcf = Channel.empty().mix(MERGE_STRELKA.out.vcf, vcf.no_intervals) // add variantcaller to meta map and remove no longer necessary field: num_intervals .map{ meta, vcf -> [ meta - meta.subMap('num_intervals') + [ variantcaller:'strelka' ], vcf ] } From 5e17e25f675bd8992d9cd8fc757eb1560fa40518 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 2 Jun 2023 16:39:17 +0200 Subject: [PATCH 2/3] FIX: join mismatch for annotation --- workflows/sarek.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index b66e175a2b..3daf99d241 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -1040,7 +1040,7 @@ workflow SAREK { vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[], []] VCF_ANNOTATE_ALL( - vcf_to_annotate, + vcf_to_annotate.map{meta, vcf -> [ meta + [ file_name: vcf.baseName ], vcf ] }, vep_fasta, params.tools, params.snpeff_genome ? "${params.snpeff_genome}.${params.snpeff_db}" : "${params.genome}.${params.snpeff_db}", From 7c83c744384b6bd2d28d23543b9c4c610c5d368f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 2 Jun 2023 16:40:21 +0200 Subject: [PATCH 3/3] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index bfd6d19f64..d9b8e44f47 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -78,6 +78,7 @@ Bierikjávrre is one of the largest lake in Sarek. - [#1055](https://github.com/nf-core/sarek/pull/1055) - Fix pattern for fasta file in the json schema - [#1058](https://github.com/nf-core/sarek/pull/1058) - Fix container declaration for VCFTOOLS as it has been updated in the registry - [#1062](https://github.com/nf-core/sarek/pull/1062) - Fix automatic restart from steps +- [#1063](https://github.com/nf-core/sarek/pull/1063) - Fix join duplication for manta/strelka ### Removed