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biopet.biopet
Commits
6bad7eaf
Commit
6bad7eaf
authored
Sep 27, 2015
by
Peter van 't Hof
Browse files
Fixed single-end runs
parent
41857e5d
Changes
2
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public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
6bad7eaf
...
...
@@ -172,7 +172,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Adds all chunkable jobs of flexiprep */
def
runTrimClip
(
R1_in
:
File
,
R2_in
:
Option
[
File
],
outDir
:
File
,
chunkarg
:
String
)
:
(
File
,
Option
[
File
],
List
[
File
])
=
{
val
chunk
=
if
(
chunkarg
.
isEmpty
||
chunkarg
.
endsWith
(
"_"
))
chunkarg
else
chunkarg
+
"_"
var
results
:
Map
[
String
,
File
]
=
Map
()
var
R1
=
R1_in
var
R2
=
R2_in
...
...
@@ -181,9 +180,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val
qcCmdR1
=
new
QcCommand
(
this
,
fastqc_R1
)
qcCmdR1
.
input
=
R1_in
qcCmdR1
.
read
=
"R1"
qcCmdR1
.
output
=
if
(
paired
)
new
File
(
"/dev/stdout"
)
else
new
File
(
outDir
,
s
"${sampleId.getOrElse("
x
")}-${libId.getOrElse("
x
")}.R1.qc.fq.gz"
)
qcCmdR1
.
output
=
if
(
paired
)
new
File
(
"/dev/stdout"
)
else
fastqR1Qc
qcCmdR1
.
isIntermediate
=
paired
||
!
keepQcFastqFiles
if
(
paired
)
{
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
6bad7eaf
...
...
@@ -31,7 +31,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
require
(
read
!=
null
)
deps
::=
out
put
deps
::=
in
put
}
override
def
defaultCoreMemory
=
2.0
...
...
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