Merge pull request #66 from nf-core/strict-syntax

Strict syntax

Author: vagkaratzas

.github/workflows/nf-test.yml

@@ -79,7 +79,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
+          - "25.10.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

CHANGELOG.md

@@ -18,7 +18,6 @@ Initial release of nf-core/proteinannotator, created with the [nf-core](https://
 - [#52](https://github.com/nf-core/proteinannotator/pull/52) - Add option to turn off InterProScan for testing
 - [#51](https://github.com/nf-core/proteinannotator/pull/51) - Update to nf-core/tools v3.3.1
 - [#47](https://github.com/nf-core/proteinannotator/pull/47) - Update metromap with more tools added from [May 2025 Hackathon](https://nf-co.re/events/2025/hackathon-boston)
-<!-- - [#43](https://github.com/nf-core/proteinannotator/pull/44) - Add [mTM-Align](https://nf-co.re/modules/mtmalign_align/) and [MMseqs2 Search](https://nf-co.re/modules/mmseqs_search/) modules -->
 - [#42](https://github.com/nf-core/proteinannotator/pull/42) - Updated to `nf-test` on GitHub Actions and in the `PULL_REQUEST_TEMPLATE.md`
 - [#13](https://github.com/nf-core/proteinannotator/pull/13) - Add nf-core seqkit/stats module
 - [#9](https://github.com/nf-core/proteinannotator/pull/9) - Add [InterProScan](https://interproscan-docs.readthedocs.io/) module

README.md

@@ -10,7 +10,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

modules.json

@@ -15,16 +15,6 @@
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
-                    "mmseqs/search": {
-                        "branch": "master",
-                        "git_sha": "38697a933bef7041bb935c9b8374d9948ce6c794",
-                        "installed_by": ["modules"]
-                    },
-                    "mtmalign/align": {
-                        "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
-                        "installed_by": ["modules"]
-                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "80cba9452fb1e9bb79884976fa1ca0e671949aa2",
@@ -71,7 +61,7 @@
                 "nf-core": {
                     "faa_seqfu_seqkit": {
                         "branch": "master",
-                        "git_sha": "15c0a7968179d3b717a9973a1c4f25beb8a9aa2b",
+                        "git_sha": "911a3c360b0ebdae4e36beaf734e6905174d3507",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
@@ -86,7 +76,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "ff506dcada6fc826ed0c641dc2ed1e98f7345fbe",
+                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
                         "installed_by": ["subworkflows"]
                     }
                 }