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biopet.biopet
Commits
fc2af339
Commit
fc2af339
authored
Sep 21, 2015
by
Peter van 't Hof
Browse files
Still executes multisample jobs when all samples are given with --sample flag
parent
ad73824f
Changes
3
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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
fc2af339
...
...
@@ -87,8 +87,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
else
Logging
.
addError
(
"Parent of output dir: '"
+
outputDir
.
getParent
+
"' is not writeable, outputdir can not be created"
)
this
match
{
case
q
:
MultiSampleQScript
if
(
q.onlySamples.nonEmpty
)
=>
logger
.
info
(
"Write
summary
is skipped because sample flag is used"
)
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
(
add
(
_
))
}
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
fc2af339
...
...
@@ -131,7 +131,7 @@ trait MultiSampleQScript extends SummaryQScript {
/** Runs addAndTrackJobs method for each sample */
final
def
addSamplesJobs
()
{
if
(
onlySamples
.
isEmpty
)
{
if
(
onlySamples
.
isEmpty
||
samples
.
forall
(
x
=>
onlySamples
.
contains
(
x
.
_1
))
)
{
samples
.
foreach
{
case
(
sampleId
,
sample
)
=>
sample
.
addAndTrackJobs
()
}
addMultiSampleJobs
()
}
else
onlySamples
.
foreach
(
sampleId
=>
samples
.
get
(
sampleId
)
match
{
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
fc2af339
...
...
@@ -136,7 +136,7 @@ trait SummaryQScript extends BiopetQScript {
addChecksum
(
file
)
this
match
{
case
q
:
MultiSampleQScript
if
(
q.onlySamples.nonEmpty
)
=>
case
q
:
MultiSampleQScript
if
q.onlySamples.nonEmpty
&&
!q.samples.forall
(
x
=>
q.onlySamples.contains
(
x.
_
1
)
)
=>
logger
.
info
(
"Write summary is skipped because sample flag is used"
)
case
_
=>
add
(
writeSummary
)
}
...
...
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