update docs, changelog and readme

CHANGELOG.md

@@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1660](https://github.com/nf-core/sarek/pull/1642) - Add `--length_required` for minimal reads length with `FASTP`
 - [1663](https://github.com/nf-core/sarek/pull/1663) - Massive conda modules update
 - [1664](https://github.com/nf-core/sarek/pull/1664) - Check if flowcell ID matches for read pair
-- [1680](https://github.com/nf-core/sarek/pull/1682) - Add `bcftools_norm` in `POST_VARIANTCALLING` for normalization of all vcf files or for concatenated germline vcfs
+- [1680](https://github.com/nf-core/sarek/pull/1682) - Add `bcftools_norm` in `POST_VARIANTCALLING` for normalization of all vcf files; edit vcf_concatenate_germline subworkflow
 - [1730](https://github.com/nf-core/sarek/pull/1730) - Enable Harshil Alignment™️ in VS Code workspace settings
 
 ### Changed

README.md

@@ -181,6 +181,7 @@ We thank the following people for their extensive assistance in the development
 - [Szilveszter Juhos](https://github.com/szilvajuhos)
 - [Tobias Koch](https://github.com/KochTobi)
 - [Winni Kretzschmar](https://github.com/winni2k)
+- [Patricie Skaláková](https://github.com/Patricie34)
 
 ## Acknowledgements
 

docs/output.md

@@ -855,6 +855,19 @@ Germline VCFs from `DeepVariant`, `FreeBayes`, `HaplotypeCaller`, `Haplotyper`,
 
 </details>
 
+All VCFs from `DeepVariant`, `FreeBayes`, `HaplotypeCaller`, `Haplotyper`, `Manta`, `bcftools mpileup`, `Strelka`, or `Tiddit` are normalized with `bcftools norm`. The field `SOURCE` is added to the VCF header to report the variant caller.
+
+<details markdown="1">
+<summary>Normalized VCF-files for normal and tumor samples</summary>
+
+**Output directory: `{outdir}/variantcalling/normalized/<sample>/`**
+
+- `<sample>.<variantcaller>.norm.vcf.gz` and `<sample>.<variantcaller>.norm.vcf.gz.tbi`
+  - VCF with tabix index
+
+</details>
+
+
 ## Variant annotation
 
 This directory contains results from the final annotation steps: two tools are used for annotation, [snpEff](http://snpeff.sourceforge.net/) and [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html). Both results can also be combined by setting `--tools merge`.