Switch SeroBA image

sanger-bentley-group · Jul 13, 2023 · ec6d519 · ec6d519
1 parent bc0a9de
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git 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+  - The fork includes critical bug fixes for SeroBA as the original repository is no longer maintained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
@@ -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'
     }
 }