diff --git a/star.wdl b/star.wdl index 9e01477a01741bd7f0e426582c416b5b833903f6..d7d3b7b595953704ab0de936b82e1ba7405fe279 100644 --- a/star.wdl +++ b/star.wdl @@ -18,6 +18,9 @@ task Star { #TODO needs to be extended for all possible output extensions Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"} + # converts String? to String for use as key (for the Map above) in output + String key = select_first([outSAMtype, "BAM SortedByCoordinate"]) + command { set -e -o pipefail mkdir -p ${sub(outFileNamePrefix, basename(outFileNamePrefix) + "$", "")} @@ -35,7 +38,7 @@ task Star { } output { - File bamFile = outFileNamePrefix + "Aligned." + samOutputNames["${outSAMtype}"] + File bamFile = outFileNamePrefix + "Aligned." + samOutputNames[key] } runtime {