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

hisat2.wdl

+version 1.0
+
+task Hisat2 {
+    input {
+        File indexDirectory
+        String indexBasename
+        File inputR1
+        File? inputR2
+        String outputBam
+        String sample
+        String library
+        String readgroup
+        String platform = "illumina"
+        Boolean downstreamTranscriptomeAssembly = true
+
+        Int threads = 1
+        Int memory = 48
+        String dockerTag = "2388ff67fc407dad75774291ca5038f40cac4be0-0"
+    }
+
+    command {
+        set -e -o pipefail
+        mkdir -p $(dirname ~{outputBam})
+        hisat2 \
+        -p ~{threads} \
+        -x ~{indexDirectory}/~{indexBasename} \
+        ~{true="-1" false="-U" defined(inputR2)} ~{inputR1} \
+        ~{"-2" + inputR2} \
+        --rg-id ~{readgroup} \
+        --rg 'SM:~{sample}' \
+        --rg 'LB:~{library}' \
+        --rg 'PL:~{platform}' \
+        ~{true="--dta" false="" downstreamTranscriptomeAssembly} \
+        | samtools sort > ~{outputBam}
+
+    }
+
+    output {
+        File bamFile = outputBam
+    }
+
+    runtime {
+        memory: (memory / threads) + 1
+        cpu: threads + 1
+        docker: "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:" + dockerTag
+    }
+}
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