Merge branch 'dev' into nf_val

nf-core · Aug 15, 2023 · 7d27bf6 · 7d27bf6
2 parents 532e9dd + 2ae0d45
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diff --git 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.)
+- [#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

diff --git a/conf/modules/haplotypecaller.config b/conf/modules/haplotypecaller.config
@@ -20,7 +20,6 @@ process {
         ext.prefix       = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) }
         ext.when         = { params.tools && params.tools.split(',').contains('haplotypecaller') }
         publishDir       = [
-            enabled: !params.joint_germline,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/"},
             pattern: "*{vcf.gz,vcf.gz.tbi}",

diff --git a/docs/output.md b/docs/output.md
@@ -392,7 +392,7 @@ If the haplotype-called VCF files are not filtered, then Sarek should be run wit
 **Output directory: `{outdir}/variantcalling/haplotypecaller/<sample>/`**
 
 - `<sample>.haplotypecaller.g.vcf.gz` and `<sample>.haplotypecaller.g.vcf.gz.tbi`
-  - VCF with tabix index
+  - gVCF with tabix index
 
 **Output directory: `{outdir}/variantcalling/haplotypecaller/joint_variant_calling/`**
 

diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml
@@ -30,3 +30,35 @@
     - path: results/variant_calling/haplotypecaller/testT/testT.haplotypecaller.g.vcf.gz.tbi
     - path: results/haplotypecaller
       should_exist: false
+- name: Run joint germline variant calling with haplotypecaller all intervals at once
+  command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --nucleotides_per_second 100
+  tags:
+    - germline
+    - joint_germline
+    - variant_calling
+  files:
+    - path: results/csv/variantcalled.csv
+      md5sum: d2dffdbd2b4f1f26a06637592d24dab3
+    - path: results/multiqc
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+      should_exist: false
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+      should_exist: false
+    - path: results/reports/bcftools/haplotypecaller/joint_variant_calling/joint_germline.bcftools_stats.txt
+    # Not stable enough
+    - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.FILTER.summary
+    # Not stable enough
+    - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.count
+    # Not stable enough
+    - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.qual
+    # Not stable enough
+    - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/haplotypecaller/testN/testN.haplotypecaller.g.vcf.gz
+    - path: results/variant_calling/haplotypecaller/testN/testN.haplotypecaller.g.vcf.gz.tbi
+    - path: results/variant_calling/haplotypecaller/testT/testT.haplotypecaller.g.vcf.gz
+    - path: results/variant_calling/haplotypecaller/testT/testT.haplotypecaller.g.vcf.gz.tbi
+    - path: results/haplotypecaller
+      should_exist: false