Merge branch 'dev' into nfschema

nf-core · Jan 8, 2025 · ee7dacd · ee7dacd
2 parents ba77921 + e4c7791
commit ee7dacd
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Showing 23 changed files with 51 additions and 47 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,14 +5,18 @@ 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
+## dev
 
 ### Added
 
+- [1759](https://github.com/nf-core/sarek/pull/1759) - Back to dev
+
 ### Changed
 
 - [1767](https://github.com/nf-core/sarek/pull/1767) - Bump nf-schema version to 2.2.1
 
+### Changed
+
 ### Fixed
 
 ### Removed

diff --git 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 <a href="https://github.com/nf-core/sarek/releases/tag/dev" target="_blank">nf-core/sarek</a>
+  This report has been generated by the <a href="https://github.com/nf-core/sarek/tree/dev" 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/3.5.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/sarek/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-sarek-methods-description":
     order: -1000

diff --git 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         = '3.6dev'
+    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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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"
                 }
             },
             [