Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
What's new
7
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Open sidebar
Mirrors
biopet.biopet
Commits
85779d49
Commit
85779d49
authored
Feb 24, 2017
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Fix report
parent
9f2f0a11
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
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
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment