Merge pull request #1640 from nf-core/dev

Release PR 3.4.4

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.

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 <a href="https://github.com/nf-core/sarek/releases/tag/3.4.3" target="_blank">nf-core/sarek</a>
+  This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.4.4" target="_blank">nf-core/sarek</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/sarek/3.4.3/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/sarek/3.4.4/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-sarek-methods-description":
     order: -1000

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:

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'
 }
 

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

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"