Merge pull request #446 from sateeshperi/dev

post-release version bump
nf-core · Oct 25, 2024 · f84ee8e · f84ee8e
2 parents cd1a02f + 8419ad3
commit f84ee8e
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Showing 20 changed files with 49 additions and 43 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,12 +1,11 @@
-bump_version: null
 lint:
   actions_ci: false
   files_exist:
     - lib/nfcore_external_java_deps.jar
     - conf/modules.config
   modules_config: false
 nf_core_version: 3.0.2
-org_path: null
+org_path:
 repository_type: pipeline
 template:
   author: Phil Ewels, Sateesh Peri
@@ -17,6 +16,6 @@ template:
   name: methylseq
   org: nf-core
   outdir: .
-  skip_features: null
-  version: 2.7.0
-update: null
+  skip_features:
+  version: 2.8.0dev
+update:
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # nf-core/methylseq
 
+## [v2.8.0](https://github.com/nf-core/methylseq/releases/tag/2.8.0) - []
+
+### Bug fixes & refactoring
+
+### Pipeline Updates
+
 ## [v2.7.0](https://github.com/nf-core/methylseq/releases/tag/2.7.0) - [2024-10-25]
 
 ### Bug fixes & refactoring

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/methylseq/releases/tag/2.7.0" target="_blank">nf-core/methylseq</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/methylseq/2.7.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/methylseq/tree/dev"
+  target="_blank">nf-core/methylseq</a> analysis pipeline. For information about how
+  to interpret these results, please see the <a href="https://nf-co.re/methylseq/dev/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-methylseq-methods-description":
     order: -1000

diff --git a/nextflow.config b/nextflow.config
@@ -289,7 +289,7 @@ manifest {
     description     = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '2.7.0'
+    version         = '2.8.0dev'
     doi             = '10.5281/zenodo.1343417'
 }
 

diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -576,4 +576,4 @@
         },
         "timestamp": "2024-10-21T17:43:14.505236122"
     }
-}
+}
diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap
@@ -30,7 +30,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -588,4 +588,4 @@
         },
         "timestamp": "2024-10-21T17:44:48.196812536"
     }
-}
+}
diff --git a/tests/bismark_hisat_rrbs.nf.test.snap b/tests/bismark_hisat_rrbs.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -581,4 +581,4 @@
         },
         "timestamp": "2024-10-21T17:48:05.852952347"
     }
-}
+}
diff --git a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -659,4 +659,4 @@
         },
         "timestamp": "2024-10-21T17:49:33.437253199"
     }
-}
+}
diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -622,4 +622,4 @@
         },
         "timestamp": "2024-10-21T17:50:56.499718354"
     }
-}
+}
diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -581,4 +581,4 @@
         },
         "timestamp": "2024-10-21T17:52:32.475797707"
     }
-}
+}
diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -651,4 +651,4 @@
         },
         "timestamp": "2024-10-21T18:10:42.065837136"
     }
-}
+}
diff --git a/tests/bismark_skip_deduplication.nf.test.snap b/tests/bismark_skip_deduplication.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -583,4 +583,4 @@
         },
         "timestamp": "2024-10-21T17:54:28.816433456"
     }
-}
+}
diff --git a/tests/bismark_skip_multiqc.nf.test.snap b/tests/bismark_skip_multiqc.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -578,4 +578,4 @@
         },
         "timestamp": "2024-10-21T17:55:48.550138313"
     }
-}
+}
diff --git a/tests/bismark_skip_trimming.nf.test.snap b/tests/bismark_skip_trimming.nf.test.snap
@@ -16,7 +16,7 @@
                     "qualimap": 2.3
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -535,4 +535,4 @@
         },
         "timestamp": "2024-10-17T11:09:41.623493366"
     }
-}
+}
diff --git a/tests/bwameth.nf.test.snap b/tests/bwameth.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -450,4 +450,4 @@
         },
         "timestamp": "2024-10-12T07:40:41.336750081"
     }
-}
+}
diff --git a/tests/bwameth_rrbs.nf.test.snap b/tests/bwameth_rrbs.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -386,7 +386,7 @@
                 "genome_results.txt:md5,58d212848ac7b7650e3bd6812a4064af"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -395,4 +395,4 @@
         },
         "timestamp": "2024-10-21T18:00:44.344954074"
     }
-}
+}
diff --git a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -498,4 +498,4 @@
         },
         "timestamp": "2024-10-21T18:01:53.259560408"
     }
-}
+}
diff --git a/tests/bwameth_skip_deduplication.nf.test.snap b/tests/bwameth_skip_deduplication.nf.test.snap
@@ -20,7 +20,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -386,7 +386,7 @@
                 "genome_results.txt:md5,478f711b8ef22e094e4d0ff7fa0dfda0"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -395,4 +395,4 @@
         },
         "timestamp": "2024-10-21T18:02:51.160774031"
     }
-}
+}
diff --git a/tests/bwameth_skip_trimming.nf.test.snap b/tests/bwameth_skip_trimming.nf.test.snap
@@ -16,7 +16,7 @@
                     "qualimap": 2.3
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -397,4 +397,4 @@
         },
         "timestamp": "2024-10-17T10:43:35.237760512"
     }
-}
+}
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -30,7 +30,7 @@
                     "cutadapt": 4.2
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.7.0"
+                    "nf-core/methylseq": "v2.8.0dev"
                 }
             },
             [
@@ -588,4 +588,4 @@
         },
         "timestamp": "2024-10-21T18:05:06.16706255"
     }
-}
+}