Commit 809e0542 authored by Peter van 't Hof's avatar Peter van 't Hof

Adding back checksum jobs

parent 363e7629
......@@ -14,14 +14,15 @@
*/
package nl.lumc.sasc.biopet.core.summary
import java.io.{ File, PrintWriter }
import java.io.{File, PrintWriter}
import java.sql.Date
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.extensions.{ CheckChecksum, Md5sum }
import nl.lumc.sasc.biopet.core.extensions.{CheckChecksum, Md5sum}
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import org.broadinstitute.gatk.queue.QScript
import nl.lumc.sasc.biopet.LastCommitHash
import nl.lumc.sasc.biopet.utils.ConfigUtils
import scala.collection.mutable
import scala.concurrent.Await
......@@ -188,6 +189,22 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
case _ => add(writeSummary)
}
qscript match {
case q: MultiSampleQScript =>
// Global level
for ((key, file) <- qscript.summaryFiles) addChecksum(file)
for ((sampleName, sample) <- q.samples) {
// Sample level
for ((key, file) <- sample.summaryFiles) addChecksum(file)
for ((libName, lib) <- sample.libraries) {
// Library level
for ((key, file) <- lib.summaryFiles) addChecksum(file)
}
}
case q => for ((key, file) <- q.summaryFiles) addChecksum(file)
}
addedJobs = true
}
}
......
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