Merge pull request #184 from nf-core/2.3.0-release

Bump version for 2.3.0 release
nf-core · Dec 23, 2024 · 7d33c65 · 7d33c65
2 parents ae6518e + d20685a
commit 7d33c65
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Showing 17 changed files with 84 additions and 40 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -14,4 +14,4 @@ template:
   name: nascent
   org: nf-core
   outdir: .
-  version: 2.3.0dev
+  version: 2.3.0
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## v2.3.0dev - [date]
+## v2.3.0 - 2024-12-23
 
 ### Added
 
@@ -13,6 +13,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#142](https://github.com/nf-core/nascent/pull/142) - Add STAR aligner
 - [#149](https://github.com/nf-core/nascent/pull/149) - Add Software citations to MultiQC
 - [#175](https://github.com/nf-core/nascent/pull/175) - Add HOMER uniqmap support
+- [a3bc907](https://github.com/nf-core/nascent/commit/a3bc907e9afd9dd2a9572798fa16fbc781c3dcb0) - Update pipeline template to [nf-core/tools 2.13.1](https://github.com/nf-core/tools/releases/tag/2.13.1)
+- [14fdbb8](https://github.com/nf-core/nascent/commit/14fdbb83fe944fc4d8d77e804f0332510d82fea4) - Update pipeline template to [nf-core/tools 3.0.0](https://github.com/nf-core/tools/releases/tag/3.0.0)
+- [b4ac8c5](https://github.com/nf-core/nascent/commit/b4ac8c5) - Update pipeline template to [nf-core/tools 3.0.1](https://github.com/nf-core/tools/releases/tag/3.0.1)
+- [a9ae47a](https://github.com/nf-core/nascent/commit/a9ae47a) - Update pipeline template to [nf-core/tools 3.0.1](https://github.com/nf-core/tools/releases/tag/3.0.2)
+- [bfcd97c](https://github.com/nf-core/nascent/commit/bfcd97c) - Update pipeline template to [nf-core/tools 3.1.0](https://github.com/nf-core/tools/releases/tag/3.1.0)
+- [7a4e356](https://github.com/nf-core/nascent/commit/7a4e356) - Update pipeline template to [nf-core/tools 3.1.1](https://github.com/nf-core/tools/releases/tag/3.1.1)
 
 ### Fixed
 

diff --git a/README.md b/README.md
@@ -94,7 +94,7 @@ For more details about the output files and reports, please refer to the
 
 nf-core/nascent was originally written by Ignacio Tripodi ([@ignaciot](https://github.com/ignaciot)) and Margaret Gruca ([@magruca](https://github.com/magruca)).
 
-The pipeline was re-written in Nextflow DSL2 by Edmund Miller ([@Emiller88](https://github.com/emiller88)) and Sruthi Suresh ([@sruthipsuresh](https://github.com/sruthipsuresh)) from [The Functional Genomics Laboratory](https://taehoonkim.org/) at [The Univeristy of Texas at Dallas](https://www.utdallas.edu/)
+The pipeline was re-written in Nextflow DSL2 by Edmund Miller ([@edmundmiller](https://github.com/edmundmiller)) and Sruthi Suresh ([@sruthipsuresh](https://github.com/sruthipsuresh)) from [The Functional Genomics Laboratory](https://taehoonkim.org/) at [The Univeristy of Texas at Dallas](https://www.utdallas.edu/)
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/nascent/tree/dev" target="_blank">nf-core/nascent</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/nascent/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/nascent/releases/tag/2.3.0"
+  target="_blank">nf-core/nascent</a> analysis pipeline. For information about how
+  to interpret these results, please see the <a href="https://nf-co.re/nascent/2.3.0/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   fastqc:
     order: 4004

diff --git a/nextflow.config b/nextflow.config
@@ -254,29 +254,36 @@ manifest {
     name            = 'nf-core/nascent'
     author          = """Edmund Miller, Ignacio Tripodi, Margaret Gruca""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
     contributors    = [
-        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
         [
             name: 'Edmund Miller',
-            affiliation: '',
+            affiliation: 'The Univeristy of Texas at Dallas',
+            email: '[email protected]',
+            github: 'edmundmiller',
+            contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: 'https://orcid.org/0000-0002-2398-0334'
+        ],
+        [
+            name: 'Sruthi Suresh',
+            affiliation: 'The Univeristy of Texas at Dallas',
             email: '',
-            github: '',
-            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            github: 'sruthipsuresh',
+            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
             orcid: ''
         ],
         [
-            name: ' Ignacio Tripodi',
+            name: 'Ignacio Tripodi',
             affiliation: '',
             email: '',
-            github: '',
-            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            github: 'ignaciot',
+            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
             orcid: ''
         ],
         [
-            name: ' Margaret Gruca',
+            name: 'Margaret Gruca',
             affiliation: '',
             email: '',
-            github: '',
-            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            github: 'magruca',
+            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
             orcid: ''
         ],
     ]
@@ -285,7 +292,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '2.3.0dev'
+    version         = '2.3.0'
     doi             = '10.5281/zenodo.7245273'
 }
 

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
diff --git a/workflows/tests/aligner/bowtie2.nf.test.snap b/workflows/tests/aligner/bowtie2.nf.test.snap
@@ -87,7 +87,7 @@
                     "subread": "2.0.1"
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             },
             [

diff --git a/workflows/tests/aligner/bwa.nf.test.snap b/workflows/tests/aligner/bwa.nf.test.snap
@@ -107,7 +107,7 @@
                     "subread": "2.0.1"
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             },
             [

diff --git a/workflows/tests/aligner/bwamem2.nf.test.snap b/workflows/tests/aligner/bwamem2.nf.test.snap
@@ -102,7 +102,7 @@
                     "subread": "2.0.1"
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             },
             [

diff --git a/workflows/tests/aligner/hisat2.nf.test.snap b/workflows/tests/aligner/hisat2.nf.test.snap
@@ -99,7 +99,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             },
             [

diff --git a/workflows/tests/aligner/star.nf.test.snap b/workflows/tests/aligner/star.nf.test.snap
@@ -90,7 +90,7 @@
                     "subread": "2.0.1"
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             },
             [
@@ -465,7 +465,7 @@
                     "subread": "2.0.1"
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             }
         ],

diff --git a/workflows/tests/inputs/gff/main.nf.test.snap b/workflows/tests/inputs/gff/main.nf.test.snap
@@ -87,7 +87,7 @@
                     "subread": "2.0.1"
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             },
             [

diff --git a/workflows/tests/inputs/gzipped_gff/main.nf.test.snap b/workflows/tests/inputs/gzipped_gff/main.nf.test.snap
@@ -87,7 +87,7 @@
                     "subread": "2.0.1"
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             },
             [

diff --git a/workflows/tests/inputs/only_gff/main.nf.test.snap b/workflows/tests/inputs/only_gff/main.nf.test.snap
@@ -90,7 +90,7 @@
                     "subread": "2.0.1"
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             },
             [

diff --git a/workflows/tests/inputs/uniqmap/main.nf.test.snap b/workflows/tests/inputs/uniqmap/main.nf.test.snap
@@ -96,7 +96,7 @@
                     "7za": 16.02
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             }
         ],

diff --git a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap
@@ -100,7 +100,7 @@
                     "subread": "2.0.1"
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             },
             [

diff --git a/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap b/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap
@@ -91,7 +91,7 @@
                     "subread": "2.0.1"
                 },
                 "Workflow": {
-                    "nf-core/nascent": "v2.3.0dev"
+                    "nf-core/nascent": "v2.3.0"
                 }
             },
             [