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biopet.biopet
Commits
8a617e00
Commit
8a617e00
authored
Mar 19, 2015
by
Wai Yi Leung
Browse files
Merge branch 'hotfix-v0.3.1'
parents
b0774761
d2efef6d
Changes
22
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pom.xml
View file @
8a617e00
...
...
@@ -9,7 +9,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
public
</relativePath>
</parent>
...
...
protected/biopet-gatk-extensions/pom.xml
View file @
8a617e00
...
...
@@ -16,7 +16,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatk
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
protected/biopet-gatk-pipelines/pom.xml
View file @
8a617e00
...
...
@@ -16,7 +16,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatk
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
protected/biopet-protected-package/pom.xml
View file @
8a617e00
...
...
@@ -16,7 +16,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatk
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
protected/pom.xml
View file @
8a617e00
...
...
@@ -11,7 +11,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetRoot
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
<artifactId>
BiopetGatk
</artifactId>
...
...
public/bam2wig/pom.xml
View file @
8a617e00
...
...
@@ -28,7 +28,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
public/bammetrics/pom.xml
View file @
8a617e00
...
...
@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
public/basty/pom.xml
View file @
8a617e00
...
...
@@ -33,7 +33,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
public/biopet-framework/pom.xml
View file @
8a617e00
...
...
@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
public/biopet-public-package/pom.xml
View file @
8a617e00
...
...
@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
public/carp/pom.xml
View file @
8a617e00
...
...
@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
public/flexiprep/pom.xml
View file @
8a617e00
...
...
@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
8a617e00
...
...
@@ -166,14 +166,16 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
var
R1
:
File
=
new
File
(
R1_in
)
var
R2
:
File
=
if
(
paired
)
new
File
(
R2_in
)
else
null
var
deps
:
List
[
File
]
=
if
(
paired
)
List
(
R1
,
R2
)
else
List
(
R1
)
var
deps_R1
:
List
[
File
]
=
R1
::
Nil
var
deps_R2
:
List
[
File
]
=
if
(
paired
)
R2
::
Nil
else
Nil
def
deps
:
List
[
File
]
=
deps_R1
:::
deps_R2
val
seqtkSeq_R1
=
SeqtkSeq
(
this
,
R1
,
swapExt
(
outDir
,
R1
,
R1_ext
,
".sanger"
+
R1_ext
),
fastqc_R1
)
seqtkSeq_R1
.
isIntermediate
=
true
add
(
seqtkSeq_R1
)
addSummarizable
(
seqtkSeq_R1
,
"seqtkSeq_R1"
)
R1
=
seqtkSeq_R1
.
output
deps
::=
R1
deps
_R1
::=
R1
if
(
paired
)
{
val
seqtkSeq_R2
=
SeqtkSeq
(
this
,
R2
,
swapExt
(
outDir
,
R2
,
R2_ext
,
".sanger"
+
R2_ext
),
fastqc_R2
)
...
...
@@ -181,17 +183,19 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
add
(
seqtkSeq_R2
)
addSummarizable
(
seqtkSeq_R2
,
"seqtkSeq_R2"
)
R2
=
seqtkSeq_R2
.
output
deps
::=
R2
deps
_R2
::=
R2
}
val
seqstat_R1
=
Seqstat
(
this
,
R1
,
outDir
)
seqstat_R1
.
isIntermediate
=
true
seqstat_R1
.
deps
=
deps_R1
add
(
seqstat_R1
)
addSummarizable
(
seqstat_R1
,
"seqstat_R1"
)
if
(
paired
)
{
val
seqstat_R2
=
Seqstat
(
this
,
R2
,
outDir
)
seqstat_R2
.
isIntermediate
=
true
seqstat_R2
.
deps
=
deps_R2
add
(
seqstat_R2
)
addSummarizable
(
seqstat_R2
,
"seqstat_R2"
)
}
...
...
@@ -201,10 +205,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val
cutadapt_R1
=
Cutadapt
(
this
,
R1
,
swapExt
(
outDir
,
R1
,
R1_ext
,
".clip"
+
R1_ext
))
cutadapt_R1
.
fastqc
=
fastqc_R1
cutadapt_R1
.
isIntermediate
=
true
cutadapt_R1
.
deps
=
deps_R1
add
(
cutadapt_R1
)
addSummarizable
(
cutadapt_R1
,
"clipping_R1"
)
R1
=
cutadapt_R1
.
fastq_output
deps
::=
R1
deps
_R1
::=
R1
outputFiles
+=
(
"cutadapt_R1_stats"
->
cutadapt_R1
.
stats_output
)
if
(
paired
)
{
...
...
@@ -212,10 +217,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
outputFiles
+=
(
"cutadapt_R2_stats"
->
cutadapt_R2
.
stats_output
)
cutadapt_R2
.
fastqc
=
fastqc_R2
cutadapt_R2
.
isIntermediate
=
true
cutadapt_R2
.
deps
=
deps_R2
add
(
cutadapt_R2
)
addSummarizable
(
cutadapt_R2
,
"clipping_R2"
)
R2
=
cutadapt_R2
.
fastq_output
deps
::=
R2
deps
_R2
::=
R2
val
fqSync
=
new
FastqSync
(
this
)
fqSync
.
refFastq
=
cutadapt_R1
.
fastq_input
...
...
@@ -230,7 +236,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
outputFiles
+=
(
"syncStats"
->
fqSync
.
outputStats
)
R1
=
fqSync
.
outputFastq1
R2
=
fqSync
.
outputFastq2
deps
:::=
R1
::
R2
::
Nil
deps_R1
::=
R1
deps_R2
::=
R2
}
}
...
...
@@ -253,13 +260,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
}
val
seqstat_R1_after
=
Seqstat
(
this
,
R1
,
outDir
)
seqstat_R1_after
.
deps
=
deps
seqstat_R1_after
.
deps
=
deps
_R1
add
(
seqstat_R1_after
)
addSummarizable
(
seqstat_R1_after
,
"seqstat_R1_after"
)
if
(
paired
)
{
val
seqstat_R2_after
=
Seqstat
(
this
,
R2
,
outDir
)
seqstat_R2_after
.
deps
=
deps
seqstat_R2_after
.
deps
=
deps
_R2
add
(
seqstat_R2_after
)
addSummarizable
(
seqstat_R2_after
,
"seqstat_R2_after"
)
}
...
...
public/gentrap/pom.xml
View file @
8a617e00
...
...
@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
View file @
8a617e00
...
...
@@ -63,20 +63,27 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
override
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"-vP"
)
+
required
(
"""\t\t"""
)
}
private
def
varscan
=
new
Mpileup2cns
(
wrapper
.
root
)
{
private
val
varscan
=
new
Mpileup2cns
(
wrapper
.
root
)
{
strandFilter
=
Option
(
0
)
outputVcf
=
Option
(
1
)
}
private
def
compress
=
new
Bgzip
(
wrapper
.
root
)
{
this
.
output
=
wrapper
.
output
}
private
val
compress
=
new
Bgzip
(
wrapper
.
root
)
private
def
index
=
new
Tabix
(
wrapper
.
root
)
{
private
val
index
=
new
Tabix
(
wrapper
.
root
)
{
input
=
compress
.
output
p
=
Option
(
"vcf"
)
}
override
def
freezeFieldValues
()
:
Unit
=
{
varscan
.
output
=
Option
(
new
File
(
wrapper
.
output
.
toString
.
stripSuffix
(
".gz"
)))
compress
.
input
=
List
(
varscan
.
output
.
get
)
compress
.
output
=
this
.
output
super
.
freezeFieldValues
()
varscan
.
qSettings
=
this
.
qSettings
varscan
.
freezeFieldValues
()
}
override
def
beforeGraph
:
Unit
=
{
require
(
output
.
toString
.
endsWith
(
".gz"
),
"Output must have a .gz file extension"
)
}
...
...
@@ -85,6 +92,6 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
// FIXME: manual trigger of commandLine for version retrieval
mpileup
.
commandLine
mpileup
.
cmdPipe
+
" | "
+
fixMpileup
.
commandLine
+
" | "
+
removeEmptyPile
.
commandLine
+
" | "
+
varscan
.
commandLine
+
"
|
"
+
compress
.
commandLine
+
" && "
+
index
.
commandLine
varscan
.
commandLine
+
"
&&
"
+
compress
.
commandLine
+
" && "
+
index
.
commandLine
}
}
public/kopisu/pom.xml
View file @
8a617e00
...
...
@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
public/mapping/pom.xml
View file @
8a617e00
...
...
@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
public/pom.xml
View file @
8a617e00
...
...
@@ -22,7 +22,7 @@
<groupId>
nl.lumc.sasc
</groupId>
<name>
Biopet
</name>
<packaging>
pom
</packaging>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<modules>
<module>
biopet-framework
</module>
...
...
public/sage/pom.xml
View file @
8a617e00
...
...
@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
public/shiva/pom.xml
View file @
8a617e00
...
...
@@ -22,7 +22,7 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.3.
0
</version>
<version>
0.3.
1
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
...
...
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