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biopet.biopet
Commits
bd6eae2c
Commit
bd6eae2c
authored
Sep 18, 2015
by
Peter van 't Hof
Browse files
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Fixed case class
parent
b21fac92
Changes
10
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10 changed files
with
19 additions
and
15 deletions
+19
-15
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+1
-1
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+1
-1
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+5
-1
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
...a/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
+1
-1
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+2
-2
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+2
-2
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+2
-2
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+1
-1
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+3
-3
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+1
-1
No files found.
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @
bd6eae2c
...
...
@@ -35,7 +35,7 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
var
bamFile
:
File
=
null
def
init
()
:
Unit
=
{
inputFiles
:+=
InputFile
(
bamFile
)
inputFiles
:+=
new
InputFile
(
bamFile
)
}
def
biopetScript
()
:
Unit
=
{
...
...
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
bd6eae2c
...
...
@@ -72,7 +72,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
/** executed before script */
def
init
()
:
Unit
=
{
inputFiles
:+=
InputFile
(
inputBam
)
inputFiles
:+=
new
InputFile
(
inputBam
)
}
/** Script to add jobs */
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
bd6eae2c
...
...
@@ -48,7 +48,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
var
outputFiles
:
Map
[
String
,
File
]
=
Map
()
protected
case
class
InputFile
(
file
:
File
,
md5
:
Option
[
String
]
=
None
)
type
InputFile
=
BiopetQScript
.
InputFile
var
inputFiles
:
List
[
InputFile
]
=
Nil
...
...
@@ -112,3 +112,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
add
(
function
)
}
}
object
BiopetQScript
{
protected
case
class
InputFile
(
file
:
File
,
md5
:
Option
[
String
]
=
None
)
}
\ No newline at end of file
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
View file @
bd6eae2c
...
...
@@ -32,7 +32,7 @@ class CheckChecksum extends InProcessFunction {
if
(
outputChecksum
!=
checksum
.
toLowerCase
)
{
logger
.
error
(
s
"Input file: '$inputFile' md5sum is not as expected, aborting pipeline"
)
System
.
exit
(
1
)
Runtime
.
getRuntime
.
halt
(
130
)
}
}
}
\ No newline at end of file
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
bd6eae2c
...
...
@@ -79,8 +79,8 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
mapping
.
input_R1
=
config
(
"R1"
)
if
(
config
.
contains
(
"R2"
))
mapping
.
input_R2
=
config
(
"R2"
)
inputFiles
:+=
InputFile
(
mapping
.
input_R1
,
config
(
"R1_md5"
))
mapping
.
input_R2
.
foreach
(
inputFiles
:+=
InputFile
(
_
,
config
(
"R2_md5"
)))
inputFiles
:+=
new
InputFile
(
mapping
.
input_R1
,
config
(
"R1_md5"
))
mapping
.
input_R2
.
foreach
(
inputFiles
:+=
new
InputFile
(
_
,
config
(
"R2_md5"
)))
mapping
.
init
()
mapping
.
biopetScript
()
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
bd6eae2c
...
...
@@ -85,8 +85,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
paired
=
input_R2
.
isDefined
inputFiles
:+=
InputFile
(
input_R1
)
input_R2
.
foreach
(
inputFiles
:+=
InputFile
(
_
))
inputFiles
:+=
new
InputFile
(
input_R1
)
input_R2
.
foreach
(
inputFiles
:+=
new
InputFile
(
_
))
if
(
input_R1
.
endsWith
(
".gz"
))
R1_name
=
input_R1
.
getName
.
substring
(
0
,
input_R1
.
getName
.
lastIndexOf
(
".gz"
))
else
if
(
input_R1
.
endsWith
(
".gzip"
))
R1_name
=
input_R1
.
getName
.
substring
(
0
,
input_R1
.
getName
.
lastIndexOf
(
".gzip"
))
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
bd6eae2c
...
...
@@ -137,8 +137,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
require
(
sampleId
.
isDefined
,
"Missing sample ID on mapping module"
)
require
(
libId
.
isDefined
,
"Missing library ID on mapping module"
)
inputFiles
:+=
InputFile
(
input_R1
)
input_R2
.
foreach
(
inputFiles
:+=
InputFile
(
_
))
inputFiles
:+=
new
InputFile
(
input_R1
)
input_R2
.
foreach
(
inputFiles
:+=
new
InputFile
(
_
))
paired
=
input_R2
.
isDefined
...
...
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @
bd6eae2c
...
...
@@ -88,7 +88,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
mapping
.
sampleId
=
Some
(
sampleId
)
protected
def
addJobs
()
:
Unit
=
{
inputFiles
:+=
InputFile
(
inputFastq
,
config
(
"R1_md5"
))
inputFiles
:+=
new
InputFile
(
inputFastq
,
config
(
"R1_md5"
))
flexiprep
.
outputDir
=
new
File
(
libDir
,
"flexiprep/"
)
flexiprep
.
input_R1
=
inputFastq
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
bd6eae2c
...
...
@@ -136,11 +136,11 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
case
(
true
,
_
)
=>
mapping
.
foreach
(
mapping
=>
{
mapping
.
input_R1
=
config
(
"R1"
)
mapping
.
input_R2
=
config
(
"R2"
)
inputFiles
:+=
InputFile
(
mapping
.
input_R1
,
config
(
"R1_md5"
))
mapping
.
input_R2
.
foreach
(
inputFiles
:+=
InputFile
(
_
,
config
(
"R2_md5"
)))
inputFiles
:+=
new
InputFile
(
mapping
.
input_R1
,
config
(
"R1_md5"
))
mapping
.
input_R2
.
foreach
(
inputFiles
:+=
new
InputFile
(
_
,
config
(
"R2_md5"
)))
})
case
(
false
,
true
)
=>
{
inputFiles
:+=
InputFile
(
config
(
"bam"
),
config
(
"bam_md5"
))
inputFiles
:+=
new
InputFile
(
config
(
"bam"
),
config
(
"bam_md5"
))
config
(
"bam_to_fastq"
,
default
=
false
).
asBoolean
match
{
case
true
=>
val
samToFastq
=
SamToFastq
(
qscript
,
config
(
"bam"
),
...
...
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
bd6eae2c
...
...
@@ -35,7 +35,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
var
inputVCF
:
File
=
_
def
init
()
:
Unit
=
{
inputFiles
:+=
InputFile
(
inputVCF
)
inputFiles
:+=
new
InputFile
(
inputVCF
)
}
override
def
defaults
=
ConfigUtils
.
mergeMaps
(
Map
(
...
...
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