Update from biotools

CITATION.cff

@@ -0,0 +1,57 @@
+cff-version: 1.2.0
+title: Pharokka
+type: software
+repository: https://github.com/gbouras13/pharokka
+identifiers:
+- type: other
+  value: pharokka
+  description: bio.tools
+license: MIT
+keywords:
+- term: Metagenomics
+  uri: http://edamontology.org/topic_3174
+- term: Sequence sites, features and motifs
+  uri: http://edamontology.org/topic_0160
+- term: Workflows
+  uri: http://edamontology.org/topic_0769
+- term: Functional, regulatory and non-coding RNA
+  uri: http://edamontology.org/topic_0659
+abstract: Pharokka is a rapid standardised annotation tool for bacteriophage genomes
+  and metagenomes.
+message: If you use this software, please cite it and the Primary publications below.
+references:
+- doi: 10.1093/bioinformatics/btac776
+  title: 'Pharokka: a fast scalable bacteriophage annotation tool.'
+  authors:
+  - first_name: George
+    last_name: Bouras
+  - first_name: Roshan
+    last_name: Nepal
+  - first_name: Ghais
+    last_name: Houtak
+  - first_name: Alkis James
+    last_name: Psaltis
+  - first_name: Peter-John
+    last_name: Wormald
+  - first_name: Sarah
+    last_name: Vreugde
+  year: 2023
+  pub_type: article
+preferred-citation:
+  doi: 10.1093/bioinformatics/btac776
+  title: 'Pharokka: a fast scalable bacteriophage annotation tool.'
+  authors:
+  - first_name: George
+    last_name: Bouras
+  - first_name: Roshan
+    last_name: Nepal
+  - first_name: Ghais
+    last_name: Houtak
+  - first_name: Alkis James
+    last_name: Psaltis
+  - first_name: Peter-John
+    last_name: Wormald
+  - first_name: Sarah
+    last_name: Vreugde
+  year: 2023
+  pub_type: article

README.md

@@ -1,12 +1,21 @@
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/gbouras13/pharokka/blob/master/run_pharokka_and_phold_and_phynteny.ipynb)
+# Protocols
 
+[![bio.tools](https://img.shields.io/badge/bio.tools-pharokka-blue.svg?labelColor=gray&logo=data:image/svg%2bxml;base64,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)](https://bio.tools/pharokka)
+![Tool Type](https://img.shields.io/badge/tool%20type-Command--line%20tool-blue.svg?labelColor=gray)
 [![Paper](https://img.shields.io/badge/paper-Bioinformatics-teal.svg?style=flat-square&maxAge=3600)](https://doi.org/10.1093/bioinformatics/btac776)
-[![CI](https://github.com/gbouras13/pharokka/actions/workflows/ci.yaml/badge.svg)](https://github.com/gbouras13/pharokka/actions/workflows/ci.yaml)
 [![BioConda Install](https://img.shields.io/conda/dn/bioconda/pharokka.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/pharokka)
+[![Bioconda Downloads](https://img.shields.io/conda/dn/bioconda/pharokka)](https://img.shields.io/conda/dn/bioconda/pharokka)
+[![Bridge](https://img.shields.io/badge/bridge-bio.tools%20%E2%86%92%20github-blue.svg?labelColor=orange&logo=data:image/svg%2bxml;base64,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)](https://bio-tools.github.io/biohackathon2025/)
+
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/gbouras13/pharokka/blob/master/run_pharokka_and_phold_and_phynteny.ipynb)
+
+
+[![CI](https://github.com/gbouras13/pharokka/actions/workflows/ci.yaml/badge.svg)](https://github.com/gbouras13/pharokka/actions/workflows/ci.yaml)
+
 [![codecov](https://codecov.io/gh/gbouras13/pharokka/branch/master/graph/badge.svg?token=4B1T2PGM9V)](https://codecov.io/gh/gbouras13/pharokka)
 
 [![Anaconda-Server Badge](https://anaconda.org/bioconda/pharokka/badges/version.svg)](https://anaconda.org/bioconda/pharokka)
-[![Bioconda Downloads](https://img.shields.io/conda/dn/bioconda/pharokka)](https://img.shields.io/conda/dn/bioconda/pharokka)
+
 [![PyPI version](https://badge.fury.io/py/pharokka.svg)](https://badge.fury.io/py/pharokka)
 [![Downloads](https://static.pepy.tech/badge/pharokka)](https://pepy.tech/project/pharokka)
 
@@ -25,7 +34,7 @@ Extra special thanks to Ghais Houtak for making Pharokka's logo.
 
 If you are looking for rapid standardised annotation of bacterial genomes, please use [Bakta](https://github.com/oschwengers/bakta). [Prokka](https://github.com/tseemann/prokka), which inspired the creation & naming of `pharokka`, is another good option, but Bakta is [Prokka's worthy successor](https://twitter.com/torstenseemann/status/1565471892840259585).
 
-# Protocols
+
 
 We have recently published a [protocols paper](https://doi.org/10.1002/cpz1.70405) in _Current Protocols_ outlining how to run Pharokka, [Phold](https://github.com/gbouras13/phold), [Phynteny](https://github.com/susiegriggo/Phynteny_transformer) for annotation and visualisation via our [Phold Plot Wasm application](https://gbouras13.github.io/phold-plot-wasm-app/).