Merge branch 'release/2.0.5'

CHANGELOG.md

@@ -1,5 +1,8 @@
 # CHANGELOG
 
+## 2.0.5
+ - Fixed a bug that would have cause the workflow to crash in the case that there were SNVs extracted from an INDEL VCF. 
+
 ## 2.0.4
  - Fixes:
  	- In situations with multiple tumours, the merged VCFs did not contain data from all tumours, they were only the merge across pipelines of each tumour. This has been corrected: there will now be a single set of merged VCFs which are a merge-by-type across all pipelines across all tumours.

Dockerfile

@@ -1,7 +1,7 @@
 FROM pancancer/seqware_whitestar_pancancer:1.1.2-actual-java8
 MAINTAINER Solomon Shorser <solomon.shorser@oicr.on.ca>
 
-ENV OXOG_WRAPPER_IMAGE_VERSION 2.0.4
+ENV OXOG_WRAPPER_IMAGE_VERSION 2.0.5
 LABEL OXOG_WRAPPER_IMAGE_VERSION $OXOG_WRAPPER_IMAGE_VERSION
 # For the storage client.
 ENV STORAGE_PROFILE=collab

README.md

@@ -40,7 +40,7 @@ To produce a full SeqWare bundle:
 
 ```
 	docker run --rm -v /datastore/:/datastore/ \
-		-v /workflows/Workflow_Bundle_OxoGWrapper_2.0.4_SeqWare_1.1.2/:/workflow/ \
+		-v /workflows/Workflow_Bundle_OxoGWrapper_2.0.5_SeqWare_1.1.2/:/workflow/ \
 		-v /var/run/docker.sock:/var/run/docker.sock \
 		-v /home/ubuntu/.gnos/:/home/ubuntu/.gnos/ \
 		-v /home/ubuntu/SomeIniFile.INI:/ini \
@@ -77,7 +77,7 @@ Populating such an INI file is a lot of work and since most of the necessary inf
 you can use the INIGenerator to produce an INI for you. It works like this:
 
 ```
-cd /workflows/Workflow_Bundle_OxoGWrapper_2.0.4_SeqWare_1.1.2/Workflow_Bundle_OxoGWrapper/2.0.4/
+cd /workflows/Workflow_Bundle_OxoGWrapper_2.0.5_SeqWare_1.1.2/Workflow_Bundle_OxoGWrapper/2.0.5/
 java -cp ./classes:./bin com.github.seqware.INIGenerator ~/BTCA-SG.BTCA_donor_A153.json
 ```
 

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>com.github.seqware</groupId>
     <artifactId>OxoGWrapper</artifactId>
-    <version>2.0.4</version>
+    <version>2.0.5</version>
     <packaging>jar</packaging>
 
     <name>OxoGWrapper</name>

src/main/java/com/github/seqware/jobgenerators/OxoGJobGenerator.java

@@ -68,7 +68,7 @@ public Job doOxoG(AbstractWorkflowDataModel workflow, String pathToTumour, Consu
 			if (!this.allowMissingFiles || (this.allowMissingFiles && vcf!=null && vcf.trim().length()>0))
 			{
 					return TemplateUtils.getRenderedTemplate(Arrays.stream(new String[][]{
-						{ "extractedSNVVCF", vcf.replaceAll("/datastore/vcf/[^/]+/", "")}, { "worfklow", pipeline.toString() }, {"extractedSNVVCFPath",vcf }
+						{ "extractedSNVVCF", vcf.replaceAll("/datastore/vcf/[^/]+/", "")}, { "workflow", pipeline.toString() }, {"extractedSNVVCFPath",vcf }
 					}).collect(this.collectToMap),"checkForExtractedSNVs.template");
 			}
 			else

src/main/resources/checkForExtractedSNVs.template

@@ -1,5 +1,5 @@
 		if (( $(zcat {{ extractedSNVVCFPath }} | grep "^[^#]" | wc -l) > 0 )) ; then
 			echo "{{ extractedSNVVCFPath }} has SNVs."
-			EXTRACTED_SNV_MOUNT=" ${EXTRACTED_SNV_MOUNT} -v  {{ extractedSNVVCFPath }}:/datafiles/VCF/{{ worfklow }}/{{ extractedSNVVCF }} "
+			EXTRACTED_SNV_MOUNT=" ${EXTRACTED_SNV_MOUNT} -v  {{ extractedSNVVCFPath }}:/datafiles/VCF/{{ workflow }}/{{ extractedSNVVCF }} "
 			EXTRACTED_SNV_FILES=" ${EXTRACTED_SNV_FILES} /datafiles/VCF/{{ workflow }}/{{ extractedSNVVCF }} "
 		fi

workflow.properties

@@ -1,3 +1,3 @@
 workflow-name=OxoGWrapper
-workflow-version=2.0.4
+workflow-version=2.0.5
 workflow-description=This workflow performs filtering and annotation on VCFs, and will also produce mini-BAMs based on the original BAMs. 

workflow/metadata.xml

@@ -1,4 +1,4 @@
-<bundle version="2.0.4">
+<bundle version="2.0.5">
   <workflow name="OxoGWrapper" version="${workflow-version}" seqware_version="${seqware-version}"
   basedir="${workflow_bundle_dir}/Workflow_Bundle_OxoGWrapper/${workflow-version}">
     <description>${workflow-description}</description>