From e4c77914d673cedff225f11c5e0926f33218ad16 Mon Sep 17 00:00:00 2001 From: Friederike Hanssen Date: Tue, 17 Dec 2024 17:59:12 +0100 Subject: [PATCH] Merge pull request #1760 from FriederikeHanssen/backtodev Back to dev --- CHANGELOG.md | 22 +++++++++++++++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- tests/aligner-bwa-mem.nf.test.snap | 4 ++-- tests/aligner-bwa-mem2.nf.test.snap | 4 ++-- tests/aligner-dragmap.nf.test.snap | 4 ++-- tests/alignment_from_everything.nf.test.snap | 2 +- tests/alignment_to_fastq.nf.test.snap | 2 +- tests/annotation_bcfann.nf.test.snap | 2 +- tests/annotation_merge.nf.test.snap | 4 ++-- tests/annotation_snpeff.nf.test.snap | 2 +- tests/annotation_vep.nf.test.snap | 2 +- tests/default.nf.test.snap | 2 +- tests/save_output_as_bam.nf.test.snap | 2 +- tests/saved_mapped.nf.test.snap | 2 +- tests/sentieon.nf.test.snap | 2 +- tests/start_from_markduplicates.nf.test.snap | 8 +++---- ...art_from_preparerecalibration.nf.test.snap | 8 +++---- tests/start_from_recalibration.nf.test.snap | 8 +++---- tests/tumor-normal-pair.nf.test.snap | 2 +- .../variant_calling_controlfreec.nf.test.snap | 12 +++++----- tests/variant_calling_strelka.nf.test.snap | 10 ++++----- tests/variant_calling_strelka_bp.nf.test.snap | 4 ++-- 23 files changed, 68 insertions(+), 46 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4e90ea7cac..f194425622 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,28 @@ 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). +## [3dev](https://github.com/nf-core/sarek/releases/tag/dev) - dev + +### Added + +- [1759](https://github.com/nf-core/sarek/pull/1759) - Back to dev + +### Changed + +### Fixed + +### Removed + +### Dependencies + +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | + +### Parameters + +| Params | Status | +| ------ | ------ | + ## [3.5.0](https://github.com/nf-core/sarek/releases/tag/3.5.0) - Áhkájiegna A set of connecting glaciers. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 4165fec686..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 1268aab63a..2efefb4199 100644 --- a/nextflow.config +++ b/nextflow.config @@ -381,7 +381,7 @@ manifest { description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '3.5.0' + version = '3.6.0dev' doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425' } diff --git a/tests/aligner-bwa-mem.nf.test.snap b/tests/aligner-bwa-mem.nf.test.snap index 9744bcceef..395ecebba9 100644 --- a/tests/aligner-bwa-mem.nf.test.snap +++ b/tests/aligner-bwa-mem.nf.test.snap @@ -17,7 +17,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -72,7 +72,7 @@ 5, { "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/aligner-bwa-mem2.nf.test.snap b/tests/aligner-bwa-mem2.nf.test.snap index 5ab17312a0..cf062a5aed 100644 --- a/tests/aligner-bwa-mem2.nf.test.snap +++ b/tests/aligner-bwa-mem2.nf.test.snap @@ -4,7 +4,7 @@ 5, { "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -60,7 +60,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/aligner-dragmap.nf.test.snap b/tests/aligner-dragmap.nf.test.snap index 3302761f2d..9cd8406f54 100644 --- a/tests/aligner-dragmap.nf.test.snap +++ b/tests/aligner-dragmap.nf.test.snap @@ -4,7 +4,7 @@ 5, { "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -64,7 +64,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/alignment_from_everything.nf.test.snap b/tests/alignment_from_everything.nf.test.snap index b82b7fbb11..26c1bf92f2 100644 --- a/tests/alignment_from_everything.nf.test.snap +++ b/tests/alignment_from_everything.nf.test.snap @@ -51,7 +51,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/alignment_to_fastq.nf.test.snap b/tests/alignment_to_fastq.nf.test.snap index 53a0512f82..0bf19803d8 100644 --- a/tests/alignment_to_fastq.nf.test.snap +++ b/tests/alignment_to_fastq.nf.test.snap @@ -51,7 +51,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/annotation_bcfann.nf.test.snap b/tests/annotation_bcfann.nf.test.snap index 0aa7d675ce..51f7072b12 100644 --- a/tests/annotation_bcfann.nf.test.snap +++ b/tests/annotation_bcfann.nf.test.snap @@ -7,7 +7,7 @@ "bcftools": 1.2 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/annotation_merge.nf.test.snap b/tests/annotation_merge.nf.test.snap index 62ea3b6aca..56c6bab95f 100644 --- a/tests/annotation_merge.nf.test.snap +++ b/tests/annotation_merge.nf.test.snap @@ -16,7 +16,7 @@ "tabix": 1.2 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -122,7 +122,7 @@ "tabix": 1.2 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/annotation_snpeff.nf.test.snap b/tests/annotation_snpeff.nf.test.snap index da7ef2d016..a9d51af6ba 100644 --- a/tests/annotation_snpeff.nf.test.snap +++ b/tests/annotation_snpeff.nf.test.snap @@ -10,7 +10,7 @@ "tabix": 1.2 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/annotation_vep.nf.test.snap b/tests/annotation_vep.nf.test.snap index d9d82cda3d..bfbda995eb 100644 --- a/tests/annotation_vep.nf.test.snap +++ b/tests/annotation_vep.nf.test.snap @@ -10,7 +10,7 @@ "tabix": 1.2 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5bf1b26c5e..f6931b8512 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -39,7 +39,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/save_output_as_bam.nf.test.snap b/tests/save_output_as_bam.nf.test.snap index 55f6083979..d2ed3f085d 100644 --- a/tests/save_output_as_bam.nf.test.snap +++ b/tests/save_output_as_bam.nf.test.snap @@ -17,7 +17,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/saved_mapped.nf.test.snap b/tests/saved_mapped.nf.test.snap index 987f214d70..648822f572 100644 --- a/tests/saved_mapped.nf.test.snap +++ b/tests/saved_mapped.nf.test.snap @@ -17,7 +17,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/sentieon.nf.test.snap b/tests/sentieon.nf.test.snap index 4c66400e96..5e89a3ae2b 100644 --- a/tests/sentieon.nf.test.snap +++ b/tests/sentieon.nf.test.snap @@ -39,7 +39,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/start_from_markduplicates.nf.test.snap b/tests/start_from_markduplicates.nf.test.snap index def63ca189..12672ddd02 100644 --- a/tests/start_from_markduplicates.nf.test.snap +++ b/tests/start_from_markduplicates.nf.test.snap @@ -16,7 +16,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -148,7 +148,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -323,7 +323,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -475,7 +475,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/start_from_preparerecalibration.nf.test.snap b/tests/start_from_preparerecalibration.nf.test.snap index bfaab47657..485f5ccc37 100644 --- a/tests/start_from_preparerecalibration.nf.test.snap +++ b/tests/start_from_preparerecalibration.nf.test.snap @@ -10,7 +10,7 @@ "gatk4": "4.5.0.0" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -78,7 +78,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -196,7 +196,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -314,7 +314,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/start_from_recalibration.nf.test.snap b/tests/start_from_recalibration.nf.test.snap index b07d2def0c..7347db8471 100644 --- a/tests/start_from_recalibration.nf.test.snap +++ b/tests/start_from_recalibration.nf.test.snap @@ -10,7 +10,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -80,7 +80,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -198,7 +198,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -310,7 +310,7 @@ "gatk4": "4.5.0.0" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/tumor-normal-pair.nf.test.snap b/tests/tumor-normal-pair.nf.test.snap index 92aef2e017..e4810e5feb 100644 --- a/tests/tumor-normal-pair.nf.test.snap +++ b/tests/tumor-normal-pair.nf.test.snap @@ -42,7 +42,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/variant_calling_controlfreec.nf.test.snap b/tests/variant_calling_controlfreec.nf.test.snap index f468d84f5c..b4b730687a 100644 --- a/tests/variant_calling_controlfreec.nf.test.snap +++ b/tests/variant_calling_controlfreec.nf.test.snap @@ -7,7 +7,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -75,7 +75,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -162,7 +162,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -302,7 +302,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -424,7 +424,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -533,7 +533,7 @@ "samtools": 1.21 }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/variant_calling_strelka.nf.test.snap b/tests/variant_calling_strelka.nf.test.snap index c72841c0f2..a2c281a07f 100644 --- a/tests/variant_calling_strelka.nf.test.snap +++ b/tests/variant_calling_strelka.nf.test.snap @@ -16,7 +16,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -221,7 +221,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -401,7 +401,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -575,7 +575,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -709,7 +709,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ diff --git a/tests/variant_calling_strelka_bp.nf.test.snap b/tests/variant_calling_strelka_bp.nf.test.snap index 7a773f06ec..c0398176b3 100644 --- a/tests/variant_calling_strelka_bp.nf.test.snap +++ b/tests/variant_calling_strelka_bp.nf.test.snap @@ -22,7 +22,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [ @@ -244,7 +244,7 @@ "vcftools": "0.1.16" }, "Workflow": { - "nf-core/sarek": "v3.5.0" + "nf-core/sarek": "v3.6.0dev" } }, [