diff --git a/CHANGELOG.md b/CHANGELOG.md
index f3e00d0863..c80878bad6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,33 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [3.4.4](https://github.com/nf-core/sarek/releases/tag/3.4.4) - Ruopsokjåkhå
+
+Ruopsokjåkhå is another peak of the Pårte massif.
+
+### Added
+
+- [1614](https://github.com/nf-core/sarek/pull/1614) - Back to dev
+- [1639](https://github.com/nf-core/sarek/pull/1639) - Bump version to prepare release
+
+### Changed
+
+- [1627](https://github.com/nf-core/sarek/pull/1627) - Correct tower reports/snpeff format
+
+### Fixed
+
+- [1623](https://github.com/nf-core/sarek/pull/1623) - Update docs to clarify vep cache folder organisation
+- [1628](https://github.com/nf-core/sarek/pull/1628) - Fix dbsnp channel mapping in germline variant calling subworkflow
+
+### Removed
+
+### Dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+
+### Parameters
+
## [3.4.3](https://github.com/nf-core/sarek/releases/tag/3.4.3) - Loametjåhkkå
Loametjåhkkå is another one of the main peaks of the Pårte massif.
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index ea1fbb0aae..e4512a603e 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/sarek/
custom_logo_title: "nf-core/sarek"
report_comment: >
- This report has been generated by the nf-core/sarek
+ This report has been generated by the nf-core/sarek
analysis pipeline. For information about how to interpret these results, please see the
- documentation.
+ documentation.
report_section_order:
"nf-core-sarek-methods-description":
order: -1000
diff --git a/docs/usage.md b/docs/usage.md
index 076cbfb04e..6a91830492 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -871,7 +871,7 @@ To use these, supply the parameters `--vep_cache` and/or `--snpeff_cache` with t
### Specify the cache location
Params `--snpeff_cache` and `--vep_cache` are used to specify the locations to the root of the annotation cache folder.
-The cache will be located within a subfolder with the path `${snpeff_species}.${snpeff_version}` for SnpEff and `${vep_species}/${vep_genome}_${vep_cache_version}` for VEP.
+The cache will be located within a subfolder with the path `${snpeff_species}.${snpeff_version}` for SnpEff and `${vep_species}/${vep_cache_version}_${vep_genome}` for VEP.
If this directory is missing, Sarek will raise an error.
For example this is a typical folder structure for `GRCh38` and `WBCel235`, with SNPeff cache version 105 and VEP cache version 110:
diff --git a/nextflow.config b/nextflow.config
index de95ae8c86..f9fa756dbb 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -396,7 +396,7 @@ manifest {
description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
- version = '3.4.3'
+ version = '3.4.4'
doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425'
}
diff --git a/subworkflows/local/bam_variant_calling_germline_all/main.nf b/subworkflows/local/bam_variant_calling_germline_all/main.nf
index 0065166bd9..deb15527d7 100644
--- a/subworkflows/local/bam_variant_calling_germline_all/main.nf
+++ b/subworkflows/local/bam_variant_calling_germline_all/main.nf
@@ -130,8 +130,8 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
fasta,
fasta_fai,
dict,
- dbsnp.map{ it -> [[id:it[0].baseName], it] },
- dbsnp_tbi.map{ it -> [[id:it[0].baseName], it] },
+ dbsnp.map{it -> [[:], it]},
+ dbsnp_tbi.map{it -> [[:], it]},
intervals)
vcf_haplotypecaller = BAM_VARIANT_CALLING_HAPLOTYPECALLER.out.vcf
diff --git a/tower.yml b/tower.yml
index acfdf00c2a..5e679d223b 100644
--- a/tower.yml
+++ b/tower.yml
@@ -51,9 +51,9 @@ reports:
display: "Control-FREEC: parsable file with information about FREEC run"
"**/reports/bcftools/*.bcftools_stats.txt":
display: "All samples raw statistics"
- "**/reports/SnpEff/*/*/*_snpEff.html":
+ "**/reports/snpeff/*/*/*_snpEff.html":
display: "Statistics and plots for the SnpEff run"
- "**/reports/SnpEff/*/*/*_snpEff.genes.txt":
+ "**/reports/snpeff/*/*/*_snpEff.genes.txt":
display: "TXT (tab separated) summary counts for variants affecting each transcript and gene"
"**/reports/EnsemblVEP/*/*/*_VEP.summary.html":
display: "Summary of the VEP run"