Merge pull request #1163 from asp8200/fix_output_docs

Correcting location of output folder for joint variant calling with h…

CHANGELOG.md

@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1145](https://github.com/nf-core/sarek/pull/1145) - Fixed Zenodo links in `README.md` and in `WorkflowMain.groovy`
 - [#1149](https://github.com/nf-core/sarek/pull/1149) - Update `Manta` modules and fix usage of `--exome` flag
 - [#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
 
 ## [3.2.3](https://github.com/nf-core/sarek/releases/tag/3.2.3) - Gällivare
 

docs/output.md

@@ -394,7 +394,7 @@ If the haplotype-called VCF files are not filtered, then Sarek should be run wit
 - `<sample>.haplotypecaller.g.vcf.gz` and `<sample>.haplotypecaller.g.vcf.gz.tbi`
   - VCF with tabix index
 
-**Output directory: `{outdir}/variantcalling/sentieon_haplotyper/joint_variant_calling/`**
+**Output directory: `{outdir}/variantcalling/haplotypecaller/joint_variant_calling/`**
 
 - `joint_germline.vcf.gz` and `joint_germline.vcf.gz.tbi`
   - VCF with tabix index