diff --git a/star.wdl b/star.wdl index 8aceb354ff858033dbf39f3fb586587bc8292112..a8e2453800a756a127738dd122f1e804e3236b4c 100644 --- a/star.wdl +++ b/star.wdl @@ -6,8 +6,8 @@ task Star { String genomeDir String outFileNamePrefix - String? outSAMtype = "BAM SortedByCoordinate" - String? readFilesCommand = "zcat" + String? outSAMtype + String? readFilesCommand Int? runThreadN String? outStd String? twopassMode @@ -24,8 +24,8 @@ task Star { --readFilesIn ${sep=',' inputR1} ${sep="," inputR2} \ --outFileNamePrefix ${outFileNamePrefix} \ --genomeDir ${genomeDir} \ - ${"--readFilesCommand " + readFilesCommand} \ - ${"--outSAMtype " + outSAMtype} \ + --outSAMtype ${default="BAM SortedByCoordinate" outSAMtype} \ + --readFilesCommand ${default="zcat" readFilesCommand} \ ${"--runThreadN " + runThreadN} \ ${"--outStd " + outStd} \ ${"--twopassMode " + twopassMode} \