From 941282da1a2cad08b93b4931f11a002e2e50504f Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Thu, 8 Aug 2024 15:05:15 +0000 Subject: [PATCH 01/10] back to dev 3.5 --- CHANGELOG.md | 17 +++++++++++++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 20 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f3e00d0863..47f50de9b6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,23 @@ 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). +## [dev](https://github.com/nf-core/sarek/tree/dev) + +### Added + +### Changed + +### Fixed + +### 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..ce1a6e388e 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/nextflow.config b/nextflow.config index de95ae8c86..6e06357d80 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 = '3.5dev' doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425' } From 56025d7cf29d370abd9bb8ae4af3e39e55d1198e Mon Sep 17 00:00:00 2001 From: Friederike Hanssen Date: Thu, 8 Aug 2024 17:07:15 +0200 Subject: [PATCH 02/10] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 47f50de9b6..bc027d6401 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- [1614](https://github.com/nf-core/sarek/pull/1614) Back to dev + ### Changed ### Fixed From 534cf130c000172fd8a80714eac74ad38bf58533 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 15 Aug 2024 14:03:38 +0200 Subject: [PATCH 03/10] Update usage.md Fix #1621 --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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: From 3e0c44c1323851a01723e825845ef7d14cd30994 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 15 Aug 2024 14:06:26 +0200 Subject: [PATCH 04/10] Update CHANGELOG.md --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bc027d6401..e786b51f10 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,12 +9,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -- [1614](https://github.com/nf-core/sarek/pull/1614) Back to dev +- [1614](https://github.com/nf-core/sarek/pull/1614) - Back to dev ### Changed ### Fixed +- [1623](https://github.com/nf-core/sarek/pull/1623) - Update docs to clarify vep cache folder organisation + ### Removed ### Dependencies From 146691d800665a4739187234c0949ca75953f8c0 Mon Sep 17 00:00:00 2001 From: chasem Date: Wed, 21 Aug 2024 13:26:25 -0500 Subject: [PATCH 05/10] changing reports/SnpEff to snpeff to match outdir format --- tower.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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" From 0de0737f3e6532ca2021665c336708038b1d3994 Mon Sep 17 00:00:00 2001 From: chasem Date: Wed, 21 Aug 2024 13:30:22 -0500 Subject: [PATCH 06/10] updating changelog with 1627 --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e786b51f10..23f4076800 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### 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 From c9a55b88db2da427e6daca84eb301ca455694e41 Mon Sep 17 00:00:00 2001 From: chasem Date: Wed, 21 Aug 2024 13:51:44 -0500 Subject: [PATCH 07/10] this adjusts the dbsnp channel mapping in variant_calling_germline_all to match variant_calling_sentieon_dnascope. null values are handled appropriately this way --- subworkflows/local/bam_variant_calling_germline_all/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 From e654579e9c0ac542856a254097ced5c878700a8c Mon Sep 17 00:00:00 2001 From: chasem Date: Wed, 21 Aug 2024 13:57:36 -0500 Subject: [PATCH 08/10] updating changelog with 1628 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e786b51f10..7a36622743 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### 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 From e0cbf05a92859af0d3d49ff641ab8b0b463dd7dc Mon Sep 17 00:00:00 2001 From: Chase Mateusiak Date: Thu, 22 Aug 2024 13:06:44 -0500 Subject: [PATCH 09/10] fix type on 1628 entry in changelog Co-authored-by: Friederike Hanssen --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7a36622743..f27a1b7c9f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### 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 +- [1628](https://github.com/nf-core/sarek/pull/1628) - Fix dbsnp channel mapping in germline variant calling subworkflow ### Removed From 261c22211d20c1662db37728cc5405bfa7b8b7e2 Mon Sep 17 00:00:00 2001 From: Friederike Hanssen Date: Mon, 2 Sep 2024 16:34:02 +0200 Subject: [PATCH 10/10] Prepare release 3.4.4 (#1639) Update version ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. - [ ] `README.md` is updated (including new tool citations and authors/contributors). --------- Co-authored-by: Maxime U Garcia --- CHANGELOG.md | 5 ++++- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c9714a2519..c80878bad6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,11 +5,14 @@ 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). -## [dev](https://github.com/nf-core/sarek/tree/dev) +## [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 diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index ce1a6e388e..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/nextflow.config b/nextflow.config index 6e06357d80..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 = '3.5dev' + version = '3.4.4' doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425' }