From f1deaf33e8fbe361b53d5df2ac9aaa6cb36d74f1 Mon Sep 17 00:00:00 2001 From: amizeranschi Date: Tue, 30 May 2023 15:16:28 +0300 Subject: [PATCH 1/2] Disable GATK filters when joint calling --- subworkflows/local/bam_variant_calling_germline_all/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/bam_variant_calling_germline_all/main.nf b/subworkflows/local/bam_variant_calling_germline_all/main.nf index b6eb00351d..04bb4859c2 100644 --- a/subworkflows/local/bam_variant_calling_germline_all/main.nf +++ b/subworkflows/local/bam_variant_calling_germline_all/main.nf @@ -122,7 +122,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL { known_snps_vqsr, intervals, intervals_bed_combined_haplotypec, - (skip_tools && skip_tools.split(',').contains('haplotypecaller_filter'))) + ((skip_tools && skip_tools.split(',').contains('haplotypecaller_filter') || joint_germline))) vcf_haplotypecaller = BAM_VARIANT_CALLING_HAPLOTYPECALLER.out.vcf versions = versions.mix(BAM_VARIANT_CALLING_HAPLOTYPECALLER.out.versions) From 6b30ea8d2feb5832ea355e1654338295b21968d1 Mon Sep 17 00:00:00 2001 From: amizeranschi Date: Tue, 30 May 2023 17:09:53 +0300 Subject: [PATCH 2/2] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d752bfe65..577c0ee2eb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -69,6 +69,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1040](https://github.com/nf-core/sarek/pull/1040) - Fix dict channel issue due to [#1032](https://github.com/nf-core/sarek/pull/1032) - [#1043](https://github.com/nf-core/sarek/pull/1043) - Fix typo in the tags.yml files from [#978](https://github.com/nf-core/sarek/pull/978) - [#1048](https://github.com/nf-core/sarek/pull/1048) - Skip tool validation on annotation to fix [#949](https://github.com/nf-core/sarek/issues/949), check that bam is bam and cram is cram [#895](https://github.com/nf-core/sarek/issues/895) +- [#1050](https://github.com/nf-core/sarek/pull/1050) - Disable GATK VCF filters when joint calling to fix [#1025](https://github.com/nf-core/sarek/issues/1025) ### Removed