From ec6d519edf62d6acdfde2f99a160a6a5728dfbc2 Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Thu, 13 Jul 2023 12:26:16 +0000
Subject: [PATCH] Switch SeroBA image

---
 README.md       | 4 +++-
 nextflow.config | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 597337b..a5f8103 100644
--- a/README.md
+++ b/README.md
@@ -421,7 +421,9 @@ This project uses open-source components. You can find the homepage or source co
 [SeroBA](https://sanger-pathogens.github.io/seroba/)
 - **SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data**. Epping L, van Tonder, AJ, Gladstone RA, GPS Consortium, Bentley SD, Page AJ, Keane JA, Microbial Genomics 2018, doi: [10.1099/mgen.0.000186](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000186)
 - License (GPL-3.0): https://github.com/sanger-pathogens/seroba/blob/master/LICENSE
-- This tool is used in `CREATE_SEROBA_DB` and `SEROTYPE` processes of the `serotype.nf` module
+- This project uses a Docker image built from a [fork](https://github.com/HarryHung/seroba)
+  - The fork includes critical bug fixes for SeroBA as the original repository is no longer maintained
+  - The Docker image provides the containerised environment for `CREATE_SEROBA_DB` and `SEROTYPE` processes of the `serotype.nf` module
 
 [Shovill](https://github.com/tseemann/shovill)
 - Torsten Seemann ([@tseemann](https://github.com/tseemann))
diff --git a/nextflow.config b/nextflow.config
index 7687a2f..a7941ac 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -100,7 +100,7 @@ process {
         container = 'staphb/kraken2:2.1.2-no-db'
     }
     withLabel: seroba_container {
-        container = 'staphb/seroba:1.0.2'
+        container = 'harryhungch/seroba:1.0.3'
     }
 }