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biopet.biopet
Commits
85779d49
Commit
85779d49
authored
Feb 24, 2017
by
Peter van 't Hof
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Fix report
parent
9f2f0a11
Changes
2
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2 changed files
with
14 additions
and
15 deletions
+14
-15
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+14
-13
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
...nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+0
-2
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
85779d49
...
...
@@ -104,19 +104,6 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
logger
.
info
(
s
"Preprocessing done for $totalCount functions"
)
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
_
=>
}
add
(
report
)
}
}
val
logDir
=
new
File
(
outputDir
,
".log"
+
File
.
separator
+
qSettings
.
runName
.
toLowerCase
)
if
(
outputDir
.
getParentFile
.
canWrite
||
(
outputDir
.
exists
&&
outputDir
.
canWrite
))
...
...
@@ -139,6 +126,20 @@ 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
_
=>
}
report
.
jobOutputFile
=
new
File
(
report
.
outputDir
,
".report.out"
)
add
(
report
)
}
}
if
(!
skipWriteDependencies
)
WriteDependencies
.
writeDependencies
(
functions
,
new
File
(
logDir
,
"graph"
))
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
View file @
85779d49
...
...
@@ -38,8 +38,6 @@ object MappingReport extends ReportBuilder {
override
def
extFiles
=
super
.
extFiles
++
List
(
"js/gears.js"
,
"js/krona-2.0.js"
,
"img/krona/loading.gif"
,
"img/krona/hidden.png"
,
"img/krona/favicon.ico"
)
.
map
(
x
=>
ExtFile
(
"/nl/lumc/sasc/biopet/pipelines/gears/report/ext/"
+
x
,
x
))
summary
.
getStatsSize
(
runId
,
Right
(
"gears"
),
Some
(
Right
(
"krakenreport"
)),
sample
=
sampleId
.
map
(
Left
(
_
)),
library
=
libId
.
map
(
Left
(
_
)))
def
krakenExecuted
:
Boolean
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
Right
(
"gears"
),
Some
(
Right
(
"krakenreport"
)),
sample
=
sampleId
.
map
(
Left
(
_
)),
library
=
libId
.
map
(
Left
(
_
))),
Duration
.
Inf
)
>=
1
...
...
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