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biopet.biopet
Commits
24d23ba1
Commit
24d23ba1
authored
Mar 07, 2015
by
bow
Browse files
Add fallback job when md5sum job fails
parent
24b411f6
Changes
1
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Inline
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
24d23ba1
...
...
@@ -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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