version bump + fix release lint + github handles for credits

.nf-core.yml

@@ -13,7 +13,7 @@ repository_type: pipeline
 template:
   author: Olga Botvinnik
   description: Generation of sequence-level annotations for amino acid sequences
-  version: 1.0.0dev
+  version: 1.0.0
   force: true
   outdir: .
   skip_features:

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).
 
-## v1.0.0dev - [date]
+## v1.0.0 - [2026/02/04]
 
 Initial release of nf-core/proteinannotator, created with the [nf-core](https://nf-co.re/) template.
 
@@ -17,15 +17,9 @@ Initial release of nf-core/proteinannotator, created with the [nf-core](https://
 - [#60](https://github.com/nf-core/proteinannotator/pull/60) - Added nf-core module `S4PRED_RUNMODEL` for secondary structure prediction (i.e., α-helix, a β-strand or a coil). (by @vagkaratzas)
 - [#59](https://github.com/nf-core/proteinannotator/pull/59) - Added nf-core qc and pre-processing subworkflow for amino acid sequences `FAA_SEQFU_SEQKIT`. (by @vagkaratzas)
 - [#57](https://github.com/nf-core/proteinannotator/pull/57) - nf-core tools template update to 3.5.1. (by @vagkaratzas)
-- [#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)
-- [#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) - Added [InterProScan](https://interproscan-docs.readthedocs.io/) module - local version
-
-### `Fixed`
-
-### `Dependencies`
-
-### `Deprecated`
+- [#52](https://github.com/nf-core/proteinannotator/pull/52) - Add option to turn off InterProScan for testing. (by @edmundmiller, @olgabot)
+- [#51](https://github.com/nf-core/proteinannotator/pull/51) - Update to nf-core/tools v3.3.1. (by @olgabot)
+- [#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). (by @olgabot)
+- [#42](https://github.com/nf-core/proteinannotator/pull/42) - Updated to `nf-test` on GitHub Actions and in the `PULL_REQUEST_TEMPLATE.md`. (by @olgabot)
+- [#13](https://github.com/nf-core/proteinannotator/pull/13) - Add nf-core seqkit/stats module. (by @olgabot, @heuermh)
+- [#9](https://github.com/nf-core/proteinannotator/pull/9) - Added [InterProScan](https://interproscan-docs.readthedocs.io/) module - local version. (by @olgabot, @heuermh, @eweizy)

assets/multiqc_config.yml

@@ -1,7 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/proteinannotator/tree/dev" target="_blank">nf-core/proteinannotator</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/proteinannotator/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/proteinannotator/releases/tag/1.0.0" target="_blank">nf-core/proteinannotator</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/proteinannotator/1.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-proteinannotator-methods-description":
     order: -1000

nextflow.config

@@ -199,8 +199,7 @@ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !pa
 
 
 // Load nf-core/proteinannotator custom profiles from different institutions.
-// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/proteinannotator.config" : "/dev/null"
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/proteinannotator.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -287,7 +286,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=25.10.0'
-    version         = '1.0.0dev'
+    version         = '1.0.0'
     doi             = ''
 }
 

ro-crate-metadata.json

@@ -21,8 +21,8 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "creativeWorkStatus": "InProgress",
-            "datePublished": "2026-01-29T12:38:19+00:00",
+            "creativeWorkStatus": "Stable",
+            "datePublished": "2026-02-04T13:01:04+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-proteinannotator_logo_dark.png\">\n    <img alt=\"nf-core/proteinannotator\" src=\"docs/images/nf-core-proteinannotator_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/proteinannotator)\n[![GitHub Actions CI Status](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[![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)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![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/)\n[![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)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinannotator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23proteinannotator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/proteinannotator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinannotator** is a bioinformatics pipeline that runs statistics of input protein fasta files and identifies\nprotein annotations such as conserved domains, functions and secondary structure features, based on their sequence data.\n\n<p>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/proteinannotator_metromap_dark.png\">\n    <img alt=\"Protein annotator metromap. Protein fasta files are summarized with `seqkit stats`, then functionally annotated with InterProScan, DIAMOND-blastp, UniFire, and Kmerseek\" src=\"docs/images/proteinannotator_metromap_light.png\">\n  </picture>\n</p>\n\n### Check quality and pre-process\n\nGenerate input amino acid sequence statistics with ([`SeqFu`](https://github.com/telatin/seqfu2/)) and pre-process them (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences) with ([`SeqKit`](https://github.com/shenwei356/seqkit/))\n\n### Annotate sequences\n\n1. Conserved domain annotation with ([`hmmer`](https://github.com/EddyRivasLab/hmmer/)) against databases\n   such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/) and [FunFam](https://download.cathdb.info/cath/releases/all-releases/)\n2. Functional annotation:\n   - ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.\n3. Predict secondary structure compositional features such as \u03b1-helices, \u03b2-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))\n4. Present QC stats for input sequences before and after initial pre-processing with ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nid,fasta\nspecies1,species1_proteins.fasta\nspecies2,species2_proteins.fasta\n```\n\nEach row represents a fasta file of proteins from a single species.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/proteinannotator \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/proteinannotator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Evangelos Karatzas](https://github.com/vagkaratzas)\n- [Martin Beracochea](https://github.com/mberacochea)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#197892e0-6893-41d7-acaa-49c7432f2b49"
+                    "@id": "#fd91eb9d-1f99-4b3e-93f2-56d5b754e7a2"
                 }
             ],
             "name": "nf-core/proteinannotator"
@@ -132,7 +132,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-01-29T12:38:19Z",
+            "dateModified": "2026-02-04T13:01:04Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -157,10 +157,10 @@
             },
             "url": [
                 "https://github.com/nf-core/proteinannotator",
-                "https://nf-co.re/proteinannotator/dev/"
+                "https://nf-co.re/proteinannotator/1.0.0/"
             ],
             "version": [
-                "1.0.0dev"
+                "1.0.0"
             ]
         },
         {
@@ -176,11 +176,11 @@
             "version": "!>=25.10.0"
         },
         {
-            "@id": "#197892e0-6893-41d7-acaa-49c7432f2b49",
+            "@id": "#fd91eb9d-1f99-4b3e-93f2-56d5b754e7a2",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#2a8f2a5c-09bf-45df-81da-ccf721407355"
+                    "@id": "#fa5732e5-538b-4606-9ac9-3caf643d317b"
                 }
             ],
             "mainEntity": {
@@ -189,7 +189,7 @@
             "name": "Test suite for nf-core/proteinannotator"
         },
         {
-            "@id": "#2a8f2a5c-09bf-45df-81da-ccf721407355",
+            "@id": "#fa5732e5-538b-4606-9ac9-3caf643d317b",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/proteinannotator",
             "resource": "repos/nf-core/proteinannotator/actions/workflows/nf-test.yml",

tests/default.nf.test.snap

@@ -43,7 +43,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/proteinannotator": "v1.0.0dev"
+                    "nf-core/proteinannotator": "v1.0.0"
                 }
             },
             [
@@ -222,6 +222,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.3"
         },
-        "timestamp": "2026-02-04T10:35:30.572658533"
+        "timestamp": "2026-02-04T12:43:32.273407057"
     }
 }