diff --git a/bedtools.wdl b/bedtools.wdl index 6ae3b3c776a52c40dc3e16bb62e4c759fc711e16..4f39e2a8907b3b8a713373a562e466905f727587 100644 --- a/bedtools.wdl +++ b/bedtools.wdl @@ -182,7 +182,7 @@ task Intersect { bedtools intersect \ -a ~{regionsA} \ -b ~{regionsB} \ - ~{true="--sorted" false="" sorted} \ + ~{true="-sorted" false="" sorted} \ ~{true="-g sorted.genome" false="" sorted} \ > ~{outputBed} }