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biopet.biopet
Commits
58d71f66
Commit
58d71f66
authored
Apr 18, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 18, 2017
Browse files
Merge branch 'develop' into Fix-BIOPET-572
parents
8106b4a6
0140969c
Changes
1
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
58d71f66
...
...
@@ -126,17 +126,21 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
})
logger
.
info
(
"Adding report"
)
this
match
{
case
q
:
MultiSampleQScript
if
q.onlySamples.nonEmpty
&&
!q.samples.forall
(
x
=>
q.onlySamples.contains
(
x.
_
1
))
=>
logger
.
info
(
"Write report is skipped because sample flag is used"
)
case
_
=>
reportClass
.
foreach
{
report
=>
for
(
f
<-
functions
)
f
match
{
case
w
:
WriteSummary
=>
report
.
deps
:+=
w
.
jobOutputFile
case
_
=>
val
writeHtmlReport
:
Boolean
=
config
(
"write_html_report"
,
default
=
true
)
if
(
writeHtmlReport
)
{
logger
.
info
(
"Adding report"
)
this
match
{
case
q
:
MultiSampleQScript
if
q.onlySamples.nonEmpty
&&
!q.samples.forall
(
x
=>
q.onlySamples.contains
(
x.
_
1
))
=>
logger
.
info
(
"Write report is skipped because sample flag is used"
)
case
_
=>
reportClass
.
foreach
{
report
=>
for
(
f
<-
functions
)
f
match
{
case
w
:
WriteSummary
=>
report
.
deps
:+=
w
.
jobOutputFile
case
_
=>
}
report
.
jobOutputFile
=
new
File
(
report
.
outputDir
,
".report.out"
)
add
(
report
)
}
report
.
jobOutputFile
=
new
File
(
report
.
outputDir
,
".report.out"
)
add
(
report
)
}
}
...
...
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