Merge pull request nf-core#572 from JoseEspinosa/dev

JoseEspinosa · web-flow · commit 447519b5018b · 2026-03-27T10:21:11.000+01:00
Bump dev version 2.1.0
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -17,4 +17,4 @@ template:
   skip_features:
     - fastqc
     - igenomes
-  version: 2.0.0
+  version: 2.1.0dev
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,18 @@
 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).
 
+## v2.1.0dev - [date]
+
+### Enhancements & fixes
+
+| Old parameter | New parameter |
+| ------------- | ------------- |
+|               |               |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present.
+> **NB:** Parameter has been **added** if just the new parameter information is present.
+> **NB:** Parameter has been **removed** if parameter information is present only for the old parameter.
+
 ## [[2.0.0](https://github.com/nf-core/proteinfold/releases/tag/2.0.0)] - 2026-03-27
 
 ### Enhancements & fixes
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/proteinfold/releases/tag/2.0.0" target="_blank">nf-core/proteinfold</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/proteinfold/2.0.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/proteinfold/tree/dev" target="_blank">nf-core/proteinfold</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/proteinfold/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-proteinfold-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
@@ -570,7 +570,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=25.10.2'
-    version         = '2.0.0'
+    version         = '2.1.0dev'
     doi             = '10.5281/zenodo.7629996'
 }
 
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
diff --git a/tests/alphafold2_download.nf.test.snap b/tests/alphafold2_download.nf.test.snap
@@ -29,7 +29,7 @@
                     "biopython": "unknown"
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -123,6 +123,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:09:42.635737909"
+        "timestamp": "2026-03-27T08:42:46.521360256"
     }
 }
diff --git a/tests/alphafold2_split.nf.test.snap b/tests/alphafold2_split.nf.test.snap
@@ -22,7 +22,7 @@
                     "biopython": "unknown"
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -73,6 +73,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:12:35.47858571"
+        "timestamp": "2026-03-27T08:45:45.745906851"
     }
 }
diff --git a/tests/alphafold3.nf.test.snap b/tests/alphafold3.nf.test.snap
@@ -27,7 +27,7 @@
                     "rdkit": "unknown"
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -108,6 +108,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:14:34.760694724"
+        "timestamp": "2026-03-27T08:49:12.687346079"
     }
 }
diff --git a/tests/boltz.nf.test.snap b/tests/boltz.nf.test.snap
@@ -18,7 +18,7 @@
                     "python": "3.8.3"
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -98,6 +98,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:15:43.464789542"
+        "timestamp": "2026-03-27T08:53:06.410999759"
     }
 }
diff --git a/tests/colabfold_download.nf.test.snap b/tests/colabfold_download.nf.test.snap
@@ -18,7 +18,7 @@
                     "sed": 4.7
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -75,6 +75,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:17:44.266981229"
+        "timestamp": "2026-03-27T08:56:29.675960575"
     }
 }
diff --git a/tests/colabfold_local.nf.test.snap b/tests/colabfold_local.nf.test.snap
@@ -19,7 +19,7 @@
                     "sed": 4.7
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -69,6 +69,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:16:34.340030626"
+        "timestamp": "2026-03-27T08:59:52.019356523"
     }
 }
diff --git a/tests/colabfold_webserver.nf.test.snap b/tests/colabfold_webserver.nf.test.snap
@@ -15,7 +15,7 @@
                     "sed": 4.7
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -65,6 +65,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:20:48.487472959"
+        "timestamp": "2026-03-27T09:02:44.668327349"
     }
 }
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -15,7 +15,7 @@
                     "biopython": "unknown"
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -68,6 +68,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:13:26.007551223"
+        "timestamp": "2026-03-27T08:35:24.77961009"
     }
 }
diff --git a/tests/esmfold.nf.test.snap b/tests/esmfold.nf.test.snap
@@ -16,7 +16,7 @@
                     "biopython": "unknown"
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -49,6 +49,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:21:39.018391209"
+        "timestamp": "2026-03-27T09:07:29.828926981"
     }
 }
diff --git a/tests/helixfold3.nf.test.snap b/tests/helixfold3.nf.test.snap
@@ -11,7 +11,7 @@
                     "python": "unknown"
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -87,6 +87,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:22:20.586950258"
+        "timestamp": "2026-03-27T09:10:21.963345902"
     }
 }
diff --git a/tests/rosettafold2na.nf.test.snap b/tests/rosettafold2na.nf.test.snap
@@ -15,7 +15,7 @@
                     "rosettafold2na": "v0.2"
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -51,6 +51,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:23:41.931720663"
+        "timestamp": "2026-03-27T09:13:14.502746624"
     }
 }
diff --git a/tests/rosettafold_all_atom.nf.test.snap b/tests/rosettafold_all_atom.nf.test.snap
@@ -12,7 +12,7 @@
                     "rosettafold-all-atom": "unknown"
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -65,6 +65,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:23:04.191225337"
+        "timestamp": "2026-03-27T09:16:06.423724852"
     }
 }
diff --git a/tests/split_fasta.nf.test.snap b/tests/split_fasta.nf.test.snap
@@ -19,7 +19,7 @@
                     "sed": 4.7
                 },
                 "Workflow": {
-                    "nf-core/proteinfold": "v2.0.0"
+                    "nf-core/proteinfold": "v2.1.0dev"
                 }
             },
             [
@@ -69,6 +69,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
         },
-        "timestamp": "2026-03-12T16:25:13.497245275"
+        "timestamp": "2026-03-27T09:19:28.818804127"
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -570,7 +570,7 @@ manifest {`
`570`	`570`	`mainScript = 'main.nf'`
`571`	`571`	`defaultBranch = 'master'`
`572`	`572`	`nextflowVersion = '!>=25.10.2'`
`573`		`- version = '2.0.0'`
	`573`	`+ version = '2.1.0dev'`
`574`	`574`	`doi = '10.5281/zenodo.7629996'`
`575`	`575`	`}`
`576`	`576`
Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,7 @@`
`29`	`29`	`"biopython": "unknown"`
`30`	`30`	`},`
`31`	`31`	`"Workflow": {`
`32`		`- "nf-core/proteinfold": "v2.0.0"`
	`32`	`+ "nf-core/proteinfold": "v2.1.0dev"`
`33`	`33`	`}`
`34`	`34`	`},`
`35`	`35`	`[`
`@@ -123,6 +123,6 @@`
`123`	`123`	`"nf-test": "0.9.3",`
`124`	`124`	`"nextflow": "25.10.4"`
`125`	`125`	`},`
`126`		`- "timestamp": "2026-03-12T16:09:42.635737909"`
	`126`	`+ "timestamp": "2026-03-27T08:42:46.521360256"`
`127`	`127`	`}`
`128`	`128`	`}`
Original file line number	Diff line number	Diff line change
`@@ -22,7 +22,7 @@`
`22`	`22`	`"biopython": "unknown"`
`23`	`23`	`},`
`24`	`24`	`"Workflow": {`
`25`		`- "nf-core/proteinfold": "v2.0.0"`
	`25`	`+ "nf-core/proteinfold": "v2.1.0dev"`
`26`	`26`	`}`
`27`	`27`	`},`
`28`	`28`	`[`
`@@ -73,6 +73,6 @@`
`73`	`73`	`"nf-test": "0.9.3",`
`74`	`74`	`"nextflow": "25.10.4"`
`75`	`75`	`},`
`76`		`- "timestamp": "2026-03-12T16:12:35.47858571"`
	`76`	`+ "timestamp": "2026-03-27T08:45:45.745906851"`
`77`	`77`	`}`
`78`	`78`	`}`
Original file line number	Diff line number	Diff line change
`@@ -27,7 +27,7 @@`
`27`	`27`	`"rdkit": "unknown"`
`28`	`28`	`},`
`29`	`29`	`"Workflow": {`
`30`		`- "nf-core/proteinfold": "v2.0.0"`
	`30`	`+ "nf-core/proteinfold": "v2.1.0dev"`
`31`	`31`	`}`
`32`	`32`	`},`
`33`	`33`	`[`
`@@ -108,6 +108,6 @@`
`108`	`108`	`"nf-test": "0.9.3",`
`109`	`109`	`"nextflow": "25.10.4"`
`110`	`110`	`},`
`111`		`- "timestamp": "2026-03-12T16:14:34.760694724"`
	`111`	`+ "timestamp": "2026-03-27T08:49:12.687346079"`
`112`	`112`	`}`
`113`	`113`	`}`
Original file line number	Diff line number	Diff line change
`@@ -18,7 +18,7 @@`
`18`	`18`	`"python": "3.8.3"`
`19`	`19`	`},`
`20`	`20`	`"Workflow": {`
`21`		`- "nf-core/proteinfold": "v2.0.0"`
	`21`	`+ "nf-core/proteinfold": "v2.1.0dev"`
`22`	`22`	`}`
`23`	`23`	`},`
`24`	`24`	`[`
`@@ -98,6 +98,6 @@`
`98`	`98`	`"nf-test": "0.9.3",`
`99`	`99`	`"nextflow": "25.10.4"`
`100`	`100`	`},`
`101`		`- "timestamp": "2026-03-12T16:15:43.464789542"`
	`101`	`+ "timestamp": "2026-03-27T08:53:06.410999759"`
`102`	`102`	`}`
`103`	`103`	`}`