diff --git a/CHANGELOG.md b/CHANGELOG.md
index b9e1102a1..fe296b015 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).
+## dev
+
+### Added
+
+- [1803](https://github.com/nf-core/sarek/pull/1803) - Back to dev
+
+### Changed
+
+### Fixed
+
+### Removed
+
+### Dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+
+### Parameters
+
+| Params | Status |
+| ------ | ------ |
+
## [3.5.1](https://github.com/nf-core/sarek/releases/tag/3.5.1) - Akkatjåkkå
Akkatjåkkå is another glacier.
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 8e69d3605..814aef8e1 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 analysis pipeline. For information about how to
- interpret these results, please see the documentation.
report_section_order:
"nf-core-sarek-methods-description":
diff --git a/nextflow.config b/nextflow.config
index d1ce54b29..0001f858f 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 = '3.5.1'
+ 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 b4360c538..395ecebba 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -72,7 +72,7 @@
5,
{
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "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 4d6bfbd08..cf062a5ae 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -60,7 +60,7 @@
"samtools": 1.21
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
diff --git a/tests/aligner-dragmap.nf.test.snap b/tests/aligner-dragmap.nf.test.snap
index 8104e4158..9cd8406f5 100644
--- a/tests/aligner-dragmap.nf.test.snap
+++ b/tests/aligner-dragmap.nf.test.snap
@@ -4,7 +4,7 @@
5,
{
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -64,7 +64,7 @@
"samtools": 1.21
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "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 c709f34f7..26c1bf92f 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": "v3.5.1"
+ "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 abb5b18d5..0bf19803d 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
diff --git a/tests/annotation_bcfann.nf.test.snap b/tests/annotation_bcfann.nf.test.snap
index 4ad6ab731..51f7072b1 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
diff --git a/tests/annotation_merge.nf.test.snap b/tests/annotation_merge.nf.test.snap
index 75fde8c98..56c6bab95 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -122,7 +122,7 @@
"tabix": 1.2
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
diff --git a/tests/annotation_snpeff.nf.test.snap b/tests/annotation_snpeff.nf.test.snap
index eb236d9ba..a9d51af6b 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
diff --git a/tests/annotation_vep.nf.test.snap b/tests/annotation_vep.nf.test.snap
index 8d8a8c710..bfbda995e 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 05c09b6f1..f6931b851 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": "v3.5.1"
+ "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 14be38aa2..d2ed3f085 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
diff --git a/tests/saved_mapped.nf.test.snap b/tests/saved_mapped.nf.test.snap
index da7f368c6..648822f57 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
diff --git a/tests/sentieon.nf.test.snap b/tests/sentieon.nf.test.snap
index 42e489fbc..5e89a3ae2 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": "v3.5.1"
+ "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 05ee60a89..12672ddd0 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -148,7 +148,7 @@
"samtools": 1.21
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -323,7 +323,7 @@
"samtools": 1.21
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -475,7 +475,7 @@
"samtools": 1.21
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "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 dbbebfdde..485f5ccc3 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -78,7 +78,7 @@
"vcftools": "0.1.16"
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -196,7 +196,7 @@
"vcftools": "0.1.16"
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -314,7 +314,7 @@
"samtools": 1.21
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "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 2b42f75e2..7347db847 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -80,7 +80,7 @@
"vcftools": "0.1.16"
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -198,7 +198,7 @@
"vcftools": "0.1.16"
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -310,7 +310,7 @@
"gatk4": "4.5.0.0"
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "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 b6f35684b..e4810e5fe 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": "v3.5.1"
+ "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 e7932a009..b4b730687 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -75,7 +75,7 @@
"samtools": 1.21
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -162,7 +162,7 @@
"samtools": 1.21
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -302,7 +302,7 @@
"samtools": 1.21
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -424,7 +424,7 @@
"samtools": 1.21
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -533,7 +533,7 @@
"samtools": 1.21
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "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 0943c3ec6..a2c281a07 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -221,7 +221,7 @@
"vcftools": "0.1.16"
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -401,7 +401,7 @@
"vcftools": "0.1.16"
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -575,7 +575,7 @@
"vcftools": "0.1.16"
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -709,7 +709,7 @@
"vcftools": "0.1.16"
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "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 aca20ac13..c0398176b 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": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[
@@ -244,7 +244,7 @@
"vcftools": "0.1.16"
},
"Workflow": {
- "nf-core/sarek": "v3.5.1"
+ "nf-core/sarek": "v3.6.0dev"
}
},
[