diff --git a/CHANGELOG.md b/CHANGELOG.md index f3e00d086..c80878bad 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 ea1fbb0aa..e4512a603 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 076cbfb04..6a9183049 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 de95ae8c8..f9fa756db 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 0065166bd..deb15527d 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 acfdf00c2..5e679d223 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"