From b8152319dce40e24a9fe122877b1b422b91613c4 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Tue, 8 Aug 2023 21:09:31 +0000 Subject: [PATCH 1/3] fix status inference --- CHANGELOG.md | 1 + tests/csv/3.0/mapped_joint_bam.csv | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1923aa3ed3..8bb1d0cf87 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1155](https://github.com/nf-core/sarek/pull/1155) - Restore proper rendering in `usage.md` - [#1163](https://github.com/nf-core/sarek/pull/1163) - Correcting location of output folder for joint variant calling with GATK's haplotypecaller - [#1169](https://github.com/nf-core/sarek/pull/1169) - Updating Sentieon-modules. (The conda-check in the Sentieon-modules was moved to the script-section. The version of Sentieon remain unchanged.) +- [#1777](https://github.com/nf-core/sarek/pull/1777) - Fix status inference when using nf-validation plugin ### Dependencies diff --git a/tests/csv/3.0/mapped_joint_bam.csv b/tests/csv/3.0/mapped_joint_bam.csv index 1dc3920b1e..689393be00 100644 --- a/tests/csv/3.0/mapped_joint_bam.csv +++ b/tests/csv/3.0/mapped_joint_bam.csv @@ -1,3 +1,3 @@ -patient,status,sample,bam,bai -testN,0,testN,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai -testT,0,testT,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai +patient,sample,bam,bai +testN,testN,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai +testT,testT,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai From 42206c518119cbee6e4e8d72cb1fbff998fc1471 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Tue, 8 Aug 2023 21:10:05 +0000 Subject: [PATCH 2/3] update schema --- assets/schema_input.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 3fbfd515d3..2431e2bbaa 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -38,7 +38,7 @@ "type": "integer", "errorMessage": "Status can only be 0 (normal) or 1 (tumor). Defaults to 0, if none is supplied.", "meta": ["status"], - "default": 0, + "default": "0", "minimum": 0, "maximum": 1 }, From 532e9ddd01ed2b5518ee46a8471508fcf4a18178 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Tue, 8 Aug 2023 21:11:37 +0000 Subject: [PATCH 3/3] typo --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8bb1d0cf87..dd8f0eb310 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,7 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1155](https://github.com/nf-core/sarek/pull/1155) - Restore proper rendering in `usage.md` - [#1163](https://github.com/nf-core/sarek/pull/1163) - Correcting location of output folder for joint variant calling with GATK's haplotypecaller - [#1169](https://github.com/nf-core/sarek/pull/1169) - Updating Sentieon-modules. (The conda-check in the Sentieon-modules was moved to the script-section. The version of Sentieon remain unchanged.) -- [#1777](https://github.com/nf-core/sarek/pull/1777) - Fix status inference when using nf-validation plugin +- [#1177](https://github.com/nf-core/sarek/pull/1177) - Fix status inference when using nf-validation plugin ### Dependencies