Merge pull request #491 from sateeshperi/dev

2.8.0 bump-version
nf-core · Dec 13, 2024 · fd4ca9e · fd4ca9e
2 parents d22aff2 + 6c868f4
commit fd4ca9e
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diff --git a/.nf-core.yml b/.nf-core.yml
@@ -16,4 +16,4 @@ template:
   name: methylseq
   org: nf-core
   outdir: .
-  version: 2.8.0dev
+  version: 2.8.0
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).
 
-## [v2.8.0](https://github.com/nf-core/methylseq/releases/tag/2.8.0) - []
+## [v2.8.0](https://github.com/nf-core/methylseq/releases/tag/2.8.0) - [2024-12-15]
 
 ### Bug fixes & refactoring
 
@@ -17,13 +17,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457)
 - 🔧 Install `fasta_index_bismark_bwameth` subworkflow from nf-core/subworkflows [#466](https://github.com/nf-core/methylseq/pull/468)
 - 🔧 Install `fastq_align_dedup_bwameth` subworkflow from nf-core/subworkflows & introduce `use_gpu` param [#467](https://github.com/nf-core/methylseq/pull/475)
-- 🔧 reorg individual configs to `conf/modules/` named configs [#459](https://github.com/nf-core/methylseq/pull/469)
+- 🔧 Re-organise & split `conf/modules.config` to `conf/modules/` & `conf/subworkflows/` individual named configs [#459](https://github.com/nf-core/methylseq/pull/469)
 - 🔧 `run_preseq` param + skip preseq/lcextrap module by default [#458](https://github.com/nf-core/methylseq/pull/470)
 - 🔧 `run_qualimap` param + skip qualimap module by default [#367](https://github.com/nf-core/methylseq/pull/471)
 - 🔧 Raised Nextflow version requirement to `24.10.2`
-- 🔧 Update the CI for pipeline-level bwameth GPU Tests [#481](https://github.com/nf-core/methylseq/pull/478)
+- 🔧 Add CI support for pipeline-level bwameth GPU Tests [#481](https://github.com/nf-core/methylseq/pull/478)
 - 🔧 create a test for samplesheet with technical replicates [#477](https://github.com/nf-core/methylseq/pull/486)
-- 🔧 Update usage and output docs [#487](https://github.com/nf-core/methylseq/pull/489)
+- 🔧 Update README, docs/usage and docs/output docs [#487](https://github.com/nf-core/methylseq/pull/489)
 
 ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27]
 

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/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>.
+  This report has been generated by the <a href="https://github.com/nf-core/methylseq/releases/tag/2.8.0"
+  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/2.8.0/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-methylseq-methods-description":
     order: -1000

diff --git a/nextflow.config b/nextflow.config
@@ -293,35 +293,35 @@ manifest {
     contributors    = [
         [
             name: 'Phil Ewels',
-            affiliation: '',
-            email: '',
+            affiliation: 'Seqera',
+            email: '[email protected]',
             github: 'https://github.com/ewels',
             contribution: ['author', 'contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            orcid: '0000-0003-4101-2502'
         ],
         [
             name: 'Sateesh Peri',
-            affiliation: '',
-            email: '',
+            affiliation: 'PeriMatrixIT',
+            email: '[email protected]',
             github: 'https://github.com/sateeshperi',
             contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            orcid: '0000-0002-9879-9070'
         ],
         [
             name: 'Felix Krueger',
-            affiliation: '',
-            email: '',
+            affiliation: 'Altos Lab',
+            email: '[email protected]',
             github: 'https://github.com/FelixKrueger',
             contribution: ['maintainer', 'contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            orcid: '0000-0002-5513-3324'
         ],
         [
             name: 'Edmund Miller',
-            affiliation: '',
-            email: '',
-            github: 'https://github.com/emiller88',
+            affiliation: 'Department of Biological Sciences and Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX 75080, USA',
+            email: '[email protected]',
+            github: 'https://github.com/edmundmiller',
             contribution: ['maintainer', 'contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            orcid: '0000-0002-2398-0334'
         ],
         [
             name: 'Rickard Hammarén',
@@ -333,11 +333,11 @@ manifest {
         ],
         [
             name: 'Alexander Peltzer',
-            affiliation: '',
-            email: '',
+            affiliation: 'Boehringer Ingelheim Pharma GmBh & Co KG',
+            email: '[email protected]',
             github: 'https://github.com/apeltzer',
             contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            orcid: '0000-0002-6503-2180'
         ],
         [
             name: 'Patrick Hüther',
@@ -349,19 +349,19 @@ manifest {
         ],
         [
             name: 'Maxime U Garcia',
-            affiliation: '',
-            email: '',
+            affiliation: 'Seqera',
+            email: '[email protected]',
             github: 'https://github.com/maxulysse',
             contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            orcid: '0000-0003-2827-9261'
         ],
     ]
     homePage        = 'https://github.com/nf-core/methylseq'
     description     = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community."""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.10.2'
-    version         = '2.8.0dev'
+    version         = '2.8.0'
     doi             = '10.5281/zenodo.1343417'
 }
 

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
diff --git a/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap b/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap
@@ -19,7 +19,7 @@
                     "gunzip": 1.1
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap
@@ -31,7 +31,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bismark_hisat_rrbs.nf.test.snap b/tests/bismark_hisat_rrbs.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

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
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bismark_run_preseq.nf.test.snap b/tests/bismark_run_preseq.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bismark_run_qualimap.nf.test.snap b/tests/bismark_run_qualimap.nf.test.snap
@@ -24,7 +24,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bismark_skip_deduplication.nf.test.snap b/tests/bismark_skip_deduplication.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bismark_skip_multiqc.nf.test.snap b/tests/bismark_skip_multiqc.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bismark_skip_trimming.nf.test.snap b/tests/bismark_skip_trimming.nf.test.snap
@@ -16,7 +16,7 @@
                     "gunzip": 1.1
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bwameth.nf.test.snap b/tests/bwameth.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap b/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap
@@ -19,7 +19,7 @@
                     "gunzip": 1.1
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bwameth_rrbs.nf.test.snap b/tests/bwameth_rrbs.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bwameth_run_qualimap.nf.test.snap b/tests/bwameth_run_qualimap.nf.test.snap
@@ -24,7 +24,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bwameth_skip_deduplication.nf.test.snap b/tests/bwameth_skip_deduplication.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bwameth_skip_trimming.nf.test.snap b/tests/bwameth_skip_trimming.nf.test.snap
@@ -16,7 +16,7 @@
                     "gunzip": 1.1
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/bwameth_use_gpu.nf.test.snap b/tests/bwameth_use_gpu.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [

diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -31,7 +31,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0dev"
+                    "nf-core/methylseq": "v2.8.0"
                 }
             },
             [