Merge pull request #1748 from FriederikeHanssen/release_350

Prepare release 3.5.0
nf-core · Dec 10, 2024 · 6f3e673 · 6f3e673
2 parents f89dfe8 + ab6ffaa
commit 6f3e673
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Showing 23 changed files with 93 additions and 91 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,9 @@ 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
+## [3.5.0](https://github.com/nf-core/sarek/releases/tag/3.5.0) - Áhkájiegna
+
+A set of connecting glaciers.
 
 ### Added
 

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/tree/dev" target="_blank">nf-core/sarek</a>
+  This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.5.0" 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/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/sarek/3.5.0/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         = '3.5.0dev'
+    version         = '3.5.0'
     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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -72,7 +72,7 @@
             5,
             {
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -110,4 +110,4 @@
         },
         "timestamp": "2024-10-08T11:23:05.203586"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -60,7 +60,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -110,4 +110,4 @@
         },
         "timestamp": "2024-10-08T11:25:00.196657"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -64,7 +64,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -117,4 +117,4 @@
         },
         "timestamp": "2024-10-08T11:28:12.076906"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -323,7 +323,7 @@
                 "test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -332,4 +332,4 @@
         },
         "timestamp": "2024-11-09T21:51:21.998984"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -323,7 +323,7 @@
                 "test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -332,4 +332,4 @@
         },
         "timestamp": "2024-11-09T17:49:40.35031"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -37,4 +37,4 @@
         },
         "timestamp": "2024-10-29T09:38:54.991004"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -122,7 +122,7 @@
                     "tabix": 1.2
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [

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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -105,4 +105,4 @@
         },
         "timestamp": "2024-10-29T10:16:00.665699"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -280,4 +280,4 @@
         },
         "timestamp": "2024-10-29T10:19:17.846465"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -322,4 +322,4 @@
         },
         "timestamp": "2024-11-09T21:41:27.897118"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -33,7 +33,7 @@
                 "reference"
             ],
             [
-                
+
             ],
             [
                 [
@@ -48,4 +48,4 @@
         },
         "timestamp": "2024-10-08T11:11:44.283548"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -33,10 +33,10 @@
                 "reference"
             ],
             [
-                
+
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -45,4 +45,4 @@
         },
         "timestamp": "2024-10-08T09:53:32.063494"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -298,4 +298,4 @@
         },
         "timestamp": "2024-12-09T10:15:55.105507"
     }
-}
+}
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": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -115,7 +115,7 @@
                 "test.sorted.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -148,7 +148,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -323,7 +323,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -475,7 +475,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.5.0"
                 }
             },
             [
@@ -630,4 +630,4 @@
         },
         "timestamp": "2024-11-09T16:18:25.238396"
     }
-}
+}