From 424d5fe075624dda2bd404664a8645e8c384b30b Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Tue, 4 Jul 2023 15:38:41 +0000
Subject: [PATCH 1/4] Protect pipeline against SeroBA failure

---
 bin/get_serotype.sh | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/bin/get_serotype.sh b/bin/get_serotype.sh
index c737d6c..633835f 100755
--- a/bin/get_serotype.sh
+++ b/bin/get_serotype.sh
@@ -1,5 +1,6 @@
 # Run SeroBA to serotype samples
-
-seroba runSerotyping "$SEROBA_DIR"/"$DATABASE" "$READ1" "$READ2" "$SAMPLE_ID"
-
-SEROTYPE=$(awk -F'\t' '{ print $2 }' ${SAMPLE_ID}/pred.tsv)
+{
+    seroba runSerotyping "$SEROBA_DIR"/"$DATABASE" "$READ1" "$READ2" "$SAMPLE_ID" && SEROTYPE=$(awk -F'\t' '{ print $2 }' ${SAMPLE_ID}/pred.tsv)
+} || {
+    SEROTYPE="SEROBA_FAILURE"
+}

From a3eb26c431a71dc929cdf3bb685cbbfd54bc000c Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Tue, 4 Jul 2023 16:07:02 +0000
Subject: [PATCH 2/4] Include SEROBA FAILURE description

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index df7cb44..597337b 100644
--- a/README.md
+++ b/README.md
@@ -268,6 +268,8 @@ The development of this pipeline is part of the GPS Project ([Global Pneumococca
   <!-- -->
   > ⚠️ If the result of `Overall_QC` of a sample is `ASSEMBLER FAILURE`, the assembler has crashed when trying to assembly the reads. You might want to re-run the sample with [another assembler](#assembly), or discard the sample if it is a low quality one.
   <!-- -->
+  > ⚠️ If the result of `Serotype` of a sample is `SEROBA FAILURE`, SeroBA has crashed when trying to serotype the sample. Please report the issue.
+  <!-- -->
   | Field | Type | Description |
   | --- | --- | --- |
   | `Sample_ID` | Identification | Sample ID based on the raw reads file name |

From bc0a9de9616be4e9ab111e24edcc9849909adbd4 Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Tue, 4 Jul 2023 16:07:18 +0000
Subject: [PATCH 3/4] Change SEROBA FAILURE message

---
 bin/get_serotype.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/get_serotype.sh b/bin/get_serotype.sh
index 633835f..b17c2de 100755
--- a/bin/get_serotype.sh
+++ b/bin/get_serotype.sh
@@ -2,5 +2,5 @@
 {
     seroba runSerotyping "$SEROBA_DIR"/"$DATABASE" "$READ1" "$READ2" "$SAMPLE_ID" && SEROTYPE=$(awk -F'\t' '{ print $2 }' ${SAMPLE_ID}/pred.tsv)
 } || {
-    SEROTYPE="SEROBA_FAILURE"
+    SEROTYPE="SEROBA FAILURE"
 }

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 4/4] 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'
     }
 }