Merge pull request #131 from biowdl/JasperBoom-patch-dockerImage

Update dockerTag to dockerImage for common.wdl

CHANGELOG.md

@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 1.0.0-dev
 ---------------------------
++ Common: Update dockerTag to dockerImage.
 + GATK: Add CombineVariants task that allows, e.g., to merge VCFs from different callers.
 + Mutect2: Add GATK tasks related to variant filtering (LearnReadOrientationModel, MergeStats, GetPileupSummaries, CalculateContamination and FilterMutectCalls).
 + Mutect2: Add "--germline-resource" and "--f1r2-tar-gz" inputs, requiring an update to GATK 4.1.2.0. 

common.wdl

@@ -77,7 +77,7 @@ task Copy {
         Boolean recursive = false
 
         # Version not that important as long as it is stable.
-        String dockerTag = "5.0.2"
+        String dockerImage = "bash:5.0.2"
     }
 
     command {
@@ -91,7 +91,7 @@ task Copy {
     }
 
     runtime {
-        docker: "bash:" + dockerTag
+        docker: dockerImage
     }
 }
 
@@ -155,7 +155,7 @@ task YamlToJson {
     input {
         File yaml
         String outputJson = basename(yaml, "\.ya?ml$") + ".json"
-        String dockerTag = "3.13-py37-slim"
+        String dockerImage = "biowdl/pyyaml:3.13-py37-slim"
     }
     command {
         set -e
@@ -174,7 +174,7 @@ task YamlToJson {
     }
 
     runtime {
-        docker: "biowdl/pyyaml:" + dockerTag
+        docker: dockerImage
     }
 }