8000 Status inference update by FriederikeHanssen · Pull Request #1177 · nf-core/sarek · GitHub
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Status inference update #1177

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Merged
merged 4 commits into from
Aug 15, 2023
Merged

Status inference update #1177

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b815231
fix status inference
FriederikeHanssen Aug 8, 2023
42206c5
update schema
FriederikeHanssen Aug 8, 2023
532e9dd
typo
FriederikeHanssen Aug 8, 2023
7d27bf6
Merge branch 'dev' into nf_val
FriederikeHanssen Aug 15, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#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.)
- [#1172](https://github.com/nf-core/sarek/pull/1172) - Publish gvcf files when all intervals are processed at once ([#764](https://github.com/nf-core/sarek/issues/764))
- [#1177](https://github.com/nf-core/sarek/pull/1177) - Fix status inference when using nf-validation plugin

### Dependencies

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2 changes: 1 addition & 1 deletion assets/schema_input.json
8000
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Expand Up @@ -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
},
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6 changes: 3 additions & 3 deletions tests/csv/3.0/mapped_joint_bam.csv
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@@ -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
0