Commit e6c8bfa8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

fixed dependencies foe summary

parent 4d479f00
......@@ -96,22 +96,25 @@ trait SummaryQScript extends BiopetQScript { qscript =>
val writeSummary = new WriteSummary(this)
def addChecksum(file: File): Unit = {
if (writeSummary.md5sum && !SummaryQScript.md5sumCache.contains(file)) {
val md5sum = new Md5sum(this) {
override def configName = "md5sum"
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))
md5sum.output = new File(outputDir, ".md5" + file.getAbsolutePath + ".md5")
writeSummary.deps :+= md5sum.output
SummaryQScript.md5sumCache += file -> md5sum.output
add(md5sum)
if (writeSummary.md5sum) {
if (!SummaryQScript.md5sumCache.contains(file)) {
val md5sum = new Md5sum(this) {
override def configName = "md5sum"
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))
md5sum.output = new File(outputDir, ".md5" + file.getAbsolutePath + ".md5")
writeSummary.deps :+= md5sum.output
SummaryQScript.md5sumCache += file -> md5sum.output
add(md5sum)
} else writeSummary.deps :+= SummaryQScript.md5sumCache(file)
}
//TODO: add more checksums types
}
......
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