Commit 24d23ba1 authored by bow's avatar bow
Browse files

Add fallback job when md5sum job fails

parent 24b411f6
......@@ -83,7 +83,12 @@ trait SummaryQScript extends BiopetQScript {
def addChecksum(file: File): Unit = {
if (writeSummary.md5sum && !SummaryQScript.md5sumCache.contains(file)) {
val md5sum = Md5sum(this, file)
val md5sum = new Md5sum(this) {
override def cmdLine: String = super.cmdLine + " || " +
required("echo") + required("error_on_capture " + input.toString) + " > " + required(output)
}
md5sum.input = file
md5sum.output = new File(file.getParentFile, file.getName + ".md5")
// Need to not write a md5 file outside the outputDir
if (!file.getAbsolutePath.startsWith(outputDir.getAbsolutePath))
......
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