Dockerize GATK. Scattering now works with containers. Tabix another docker image.

gatk.wdl

@@ -15,6 +15,7 @@ task ApplyBQSR {
 
         Int memory = 4
         Float memoryMultiplier = 3.0
+        String dockerTag = "3.8--5"
     }
 
     String toolCommand = if defined(gatkJar)
@@ -48,6 +49,7 @@ task ApplyBQSR {
     }
 
     runtime {
+        docker: "quay.io/biocontainers/gatk:" + dockerTag
         memory: ceil(memory * memoryMultiplier)
     }
 }
@@ -66,6 +68,7 @@ task BaseRecalibrator {
         Reference reference
         Int memory = 4
         Float memoryMultiplier = 3.0
+        String dockerTag = "3.8--5"
     }
 
     Array[File]+ knownIndelsSitesVCFsArg = flatten([
@@ -95,6 +98,7 @@ task BaseRecalibrator {
     }
 
     runtime {
+        docker: "quay.io/biocontainers/gatk:" + dockerTag
         memory: ceil(memory * memoryMultiplier)
     }
 }
@@ -114,6 +118,7 @@ task CombineGVCFs {
 
         Int memory = 4
         Float memoryMultiplier = 3.0
+        String dockerTag = "3.8--5"
     }
 
     String toolCommand = if defined(gatkJar)
@@ -139,6 +144,7 @@ task CombineGVCFs {
     }
 
     runtime {
+        docker: "quay.io/biocontainers/gatk:" + dockerTag
         memory: ceil(memory * memoryMultiplier)
     }
 }
@@ -153,6 +159,7 @@ task GatherBqsrReports {
 
         Int memory = 4
         Float memoryMultiplier = 3.0
+        String dockerTag = "3.8--5"
     }
 
     String toolCommand = if defined(gatkJar)
@@ -173,6 +180,7 @@ task GatherBqsrReports {
     }
 
     runtime {
+        docker: "quay.io/biocontainers/gatk:" + dockerTag
         memory: ceil(memory * memoryMultiplier)
     }
 }
@@ -194,6 +202,7 @@ task GenotypeGVCFs {
 
         Int memory = 6
         Float memoryMultiplier = 2.0
+        String dockerTag = "3.8--5"
     }
 
     File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else ""
@@ -224,7 +233,8 @@ task GenotypeGVCFs {
         }
     }
 
-    runtime{
+    runtime {
+        docker: "quay.io/biocontainers/gatk:" + dockerTag
         memory: ceil(memory * memoryMultiplier)
     }
 }
@@ -245,6 +255,7 @@ task HaplotypeCallerGvcf {
 
         Int memory = 4
         Float memoryMultiplier = 3
+        String dockerTag = "3.8--5"
     }
 
     File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else ""
@@ -275,6 +286,7 @@ task HaplotypeCallerGvcf {
     }
 
     runtime {
+        docker: "quay.io/biocontainers/gatk:" + dockerTag
         memory: ceil(memory * memoryMultiplier)
     }
 }
@@ -294,6 +306,7 @@ task MuTect2 {
         String? gatkJar
         Int memory = 4
         Float memoryMultiplier = 3
+        String dockerTag = "3.8--5"
     }
 
     String toolCommand = if defined(gatkJar)
@@ -321,6 +334,7 @@ task MuTect2 {
     }
 
     runtime {
+        docker: "quay.io/biocontainers/gatk:" + dockerTag
         memory: ceil(memory * memoryMultiplier)
     }
 }
@@ -337,6 +351,7 @@ task SplitNCigarReads {
 
         Int memory = 4
         Float memoryMultiplier = 4
+        String dockerTag = "3.8--5"
     }
 
     String toolCommand = if defined(gatkJar)
@@ -362,6 +377,7 @@ task SplitNCigarReads {
     }
 
     runtime {
+        docker: "quay.io/biocontainers/gatk:" + dockerTag
         memory: ceil(memory * memoryMultiplier)
     }
 }