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biopet.biopet
Commits
809e0542
Commit
809e0542
authored
Mar 10, 2017
by
Peter van 't Hof
Browse files
Adding back checksum jobs
parent
363e7629
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
809e0542
...
...
@@ -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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