Merge pull request #2 from biowdl/star

Star

.gitignore

+.idea/

star.wdl

+task Star {
+    String? preCommand
+
+    Array[File] inputR1
+    Array[File]? inputR2
+    String genomeDir
+    String outFileNamePrefix
+
+    String? outSAMtype = "BAM SortedByCoordinate"
+    String? readFilesCommand = "zcat"
+    Int? runThreadN
+    String? outStd
+    String? twopassMode
+    Array[String]? outSAMattrRGline
+
+    #TODO needs to be extended for all possible output extensions
+    Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"}
+
+    command {
+        set -e -o pipefail
+        mkdir -p ${sub(outFileNamePrefix, basename(outFileNamePrefix) + "$", "")}
+        ${preCommand}
+        STAR \
+        --readFilesIn ${sep=',' inputR1} ${sep="," inputR2} \
+        --outFileNamePrefix ${outFileNamePrefix} \
+        --genomeDir ${genomeDir} \
+        ${"--readFilesCommand " + readFilesCommand} \
+        ${"--outSAMtype " + outSAMtype} \
+        ${"--runThreadN " + runThreadN} \
+        ${"--outStd " + outStd} \
+        ${"--twopassMode " + twopassMode} \
+        ${true="--outSAMattrRGline " false="" defined(outSAMattrRGline)} ${sep=" , " outSAMattrRGline}
+    }
+
+    output {
+        File bamFile = outFileNamePrefix + "Aligned." +  samOutputNames["${outSAMtype}"]
+    }
+
+    runtime {
+        threads: runThreadN
+    }
+}
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