nf-core · vagkaratzas · May 5, 2026 · May 5, 2026 · May 5, 2026 · May 5, 2026
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).
 
-## v1.1.0dev - [date]
+## v1.1.0dev - [2026/05/05]
 
 ### `Added`
 
@@ -13,8 +13,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#93](https://github.com/nf-core/proteinfamilies/pull/93) - nf-core tools template update to 4.0.2. (by @vagkaratzas)
 - [#85](https://github.com/nf-core/proteinannotator/pull/85) - `test_full.config` input samplesheet path is now set properly. (by @vagkaratzas)
 
+### `Dependencies`
+
+| Tool    | Previous version | New version |
+| ------- | ---------------- | ----------- |
+| aria2   | 1.36.0           | 1.37.0      |
+| multiqc | 1.33             | 1.34        |
+
 ## v1.0.0 - Yellow Saiga - [2026/02/09]
 
 Initial release of nf-core/proteinannotator, created with the [nf-core](https://nf-co.re/) template.

diff --git a/modules.json b/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "aria2": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "hmmer/hmmsearch": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "interproscan": {
                         "branch": "master",
-                        "git_sha": "50ab4e0a9616556589152fef559b50a6e86c326b",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -27,37 +27,37 @@
                     },
                     "s4pred/runmodel": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "seqfu/stats": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
                     "seqkit/replace": {
                         "branch": "master",
-                        "git_sha": "2eccc519c7d25e24c8ef2a5a94062630b8383daf",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
                     "seqkit/rmdup": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
                     "seqkit/seq": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
                     "seqkit/stats": {
                         "branch": "master",
-                        "git_sha": "28935b89b7e1f19e835f8c6e4c8322d4b505dded",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     }
                 }
@@ -66,7 +66,7 @@
                 "nf-core": {
                     "faa_seqfu_seqkit": {
                         "branch": "master",
-                        "git_sha": "2eccc519c7d25e24c8ef2a5a94062630b8383daf",
+                        "git_sha": "bf70cbf44b42ff4a81afcb673fcef604f5ef3a85",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {

diff --git a/modules/nf-core/aria2/environment.yml b/modules/nf-core/aria2/environment.yml
diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf
diff --git a/modules/nf-core/aria2/meta.yml b/modules/nf-core/aria2/meta.yml
diff --git a/modules/nf-core/aria2/tests/main.nf.test b/modules/nf-core/aria2/tests/main.nf.test
diff --git a/modules/nf-core/aria2/tests/main.nf.test.snap b/modules/nf-core/aria2/tests/main.nf.test.snap
diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf
diff --git a/modules/nf-core/interproscan/main.nf b/modules/nf-core/interproscan/main.nf
diff --git a/modules/nf-core/s4pred/runmodel/main.nf b/modules/nf-core/s4pred/runmodel/main.nf