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

samtools.wdl

@@ -7,6 +7,7 @@ task BgzipAndIndex {
         File inputFile
         String outputDir
         String type = "vcf"
+        String dockerTag = "0.2.6--ha92aebf_0"
     }
 
     String outputGz = outputDir + "/" + basename(inputFile) + ".gz"
@@ -20,6 +21,10 @@ task BgzipAndIndex {
         File compressed = outputGz
         File index = outputGz + ".tbi"
     }
+
+    runtime {
+        docker: "quay.io/biocontainers/tabix:" + dockerTag
+    }
 }
 
 task Index {
@@ -185,6 +190,7 @@ task Tabix {
     input {
         String inputFile
         String type = "vcf"
+        String dockerTag = "0.2.6--ha92aebf_0"
     }
 
     command {
@@ -194,6 +200,10 @@ task Tabix {
     output {
         File index = inputFile + ".tbi"
     }
+
+    runtime {
+        docker: "quay.io/biocontainers/tabix:" + dockerTag
+    }
 }
 
 task View {