Merge pull request #5 from DKFZ-ODCF/check-executibility

Check executibility

IndelCallingWorkflow.iml

@@ -1,5 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <module version="4">
+  <component name="FacetManager">
+    <facet type="Python" name="Python">
+      <configuration sdkName="Python 2.7 (AlignmentAndQCWorkflows)" />
+    </facet>
+  </component>
   <component name="NewModuleRootManager" inherit-compiler-output="true">
     <content url="file://$MODULE_DIR$">
       <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
@@ -13,6 +18,9 @@
     <orderEntry type="module" module-name="Roddy" />
     <orderEntry type="module" module-name="RoddyToolLib" />
     <orderEntry type="library" name="Gradle: org.codehaus.groovy:groovy-all:2.4.9" level="project" />
-    <orderEntry type="module" module-name="COWorkflowsBasePlugin_1.1.0" />
+    <orderEntry type="library" name="R User Library" level="project" />
+    <orderEntry type="library" name="R Skeletons" level="application" />
+    <orderEntry type="library" name="Python 2.7 (AlignmentAndQCWorkflows) interpreter library" level="application" />
+    <orderEntry type="module" module-name="COWorkflowsBasePlugin_1.4.1" />
   </component>
 </module>

README.md

@@ -52,12 +52,35 @@ There are quite extensive requirements in annotation etc. data required for the
 | extractSamplesFromOutputFiles | true | |
 | CHROMOSOME_INDICES | empty | Bash-array of chromosome names to which the analysis should be restricted |
 
+Since version 2.2.0 the workflow uses the [COWorkflowsBasePlugin](https://github.com/DKFZ-ODCF/COWorkflowsBasePlugin) 1.4.1+ with an alternative algorithm for extracting sample names from BAM files.
 
 # Example call
 
 TBD
 
 # Changelist
+
+* Version update to 2.2.0
+
+  * Upgrade from [COWorkflowsBasePlugin](https://github.com/DKFZ-ODCF/COWorkflowsBasePlugin) 1.1.0 to 1.4.1
+  * Executability check for `REFERENCE_GENOME` variable (file accessible from submission host)
+
+* Version update to 2.1.0-1
+
+  * Added gnomAD exomes
+  * Check REF_genome for BAM files
+  * Check BAM file readability
+  * Added local controls
+  * Adding python script for parsing MNPs
+
+* Version update to 2.0.0-2
+
+  * Restricting screenshot generation to 100
+
+* Version update to 2.0.0-1
+
+  * README update
+
 * Version update to 2.0.0
 
   - TiNDA workflow was updated

buildinfo.txt

@@ -1,2 +1,2 @@
-dependson=COWorkflowsBasePlugin:1.1.0
-RoddyAPIVersion=3.0
+dependson=COWorkflowsBasePlugin:1.4.1
+RoddyAPIVersion=3.5

buildversion.txt

@@ -1,2 +1,2 @@
-2.1
+2.2
 0