Merge pull request #56 from HarryHung/dev

Release 0.8.2

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 |
@@ -419,7 +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+  - The fork includes critical bug fixes for SeroBA as the original repository is no longer maintained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))

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"
+}

main.nf

@@ -1,7 +1,7 @@
 #!/usr/bin/env nextflow
 
 // Version of this release
-pipelineVersion = '0.8.1'
+pipelineVersion = '0.8.2'
 
 // Import workflow modules
 include { PIPELINE } from "$projectDir/workflows/pipeline"

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'
     }
 }