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biopet.biopet
Commits
adb6ffe1
Commit
adb6ffe1
authored
Sep 28, 2015
by
Peter van 't Hof
Browse files
Changed own vmem
parent
f42be845
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
adb6ffe1
...
...
@@ -97,10 +97,11 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
if
(
jobOutputFile
==
null
&&
firstOutput
!=
null
)
jobOutputFile
=
new
File
(
firstOutput
.
getAbsoluteFile
.
getParent
,
"."
+
firstOutput
.
getName
+
"."
+
configName
+
".out"
)
if
(
threads
==
0
)
threads
=
getThreads
(
defaultThreads
)
+
pipesJobs
.
map
(
_
.
threads
).
map
(
i
=>
if
(
i
==
0
)
1
else
i
).
sum
val
ownThreads
=
getThreads
(
defaultThreads
)
if
(
threads
==
0
)
threads
=
ownThreads
+
pipesJobs
.
map
(
_
.
threads
).
map
(
i
=>
if
(
i
==
0
)
1
else
i
).
sum
if
(
threads
>
1
)
nCoresRequest
=
Option
(
threads
)
_coreMemory
=
config
(
"core_memory"
,
default
=
defaultCoreMemory
+
_coreMemory
=
config
(
"core_memory"
,
default
=
(
defaultCoreMemory
*
(
ownThreads
.
toDouble
/
this
.
threads
.
toDouble
))
+
pipesJobs
.
map
(
job
=>
job
.
coreMemeory
*
(
job
.
threads
.
toDouble
/
this
.
threads
.
toDouble
)).
sum
).
asDouble
+
(
0.5
*
retry
)
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
adb6ffe1
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryQScript
,
Summarizable
}
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryQScript
,
Summarizable
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
BiopetPipe
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Gzip
,
Sickle
,
Cutadapt
}
import
nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
...
...
@@ -43,11 +43,11 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
override
def
addToQscriptSummary
(
qscript
:
SummaryQScript
,
name
:
String
)
:
Unit
=
{
clip
match
{
case
Some
(
job
)
=>
qscript
.
addSummarizable
(
job
,
s
"clipping_$read"
)
case
_
=>
case
_
=>
}
trim
match
{
case
Some
(
job
)
=>
qscript
.
addSummarizable
(
job
,
s
"trimming_$read"
)
case
_
=>
case
_
=>
}
}
...
...
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