Added mkdir step

9ddfbe5b · pjvan_thof · 99dbe5f3 · 9ddfbe5b
Commit 9ddfbe5b authored 6 years ago by pjvan_thof
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -54,6 +54,7 @@ task Flagstat {
    command {
        set -e -o pipefail
        ${preCommand}
+        mkdir -p $(dirname ${outputPath})
        samtools flagstat ${inputBam} > ${outputPath}
    }