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Mirrors
biopet.biopet
Commits
ad0c55bc
Commit
ad0c55bc
authored
Feb 03, 2015
by
bow
Browse files
Rename libraryId -> libId for consistency
parent
daf3d591
Changes
11
Hide whitespace changes
Inline
Side-by-side
protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
ad0c55bc
...
...
@@ -33,7 +33,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
lib
rary
Id
:
String
)
extends
AbstractLibrary
(
lib
rary
Id
)
{
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
protected
def
addJobs
()
:
Unit
=
{}
}
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
ad0c55bc
...
...
@@ -43,10 +43,10 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
lib
rary
Id
:
String
)
extends
AbstractLibrary
(
lib
rary
Id
)
{
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
val
mapping
=
new
Mapping
(
qscript
)
mapping
.
sampleId
=
sampleId
mapping
.
lib
rary
Id
=
lib
rary
Id
mapping
.
libId
=
libId
mapping
.
outputDir
=
libDir
+
"/variantcalling/"
/** Library variantcalling */
...
...
@@ -67,8 +67,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
if
(!
bamFile
.
exists
)
throw
new
IllegalStateException
(
"Bam in config does not exist, file: "
+
bamFile
)
if
(
config
(
"bam_to_fastq"
,
default
=
false
).
asBoolean
)
{
val
samToFastq
=
SamToFastq
(
qscript
,
bamFile
,
libDir
+
sampleId
+
"-"
+
lib
rary
Id
+
".R1.fastq"
,
libDir
+
sampleId
+
"-"
+
lib
rary
Id
+
".R2.fastq"
)
val
samToFastq
=
SamToFastq
(
qscript
,
bamFile
,
libDir
+
sampleId
+
"-"
+
libId
+
".R1.fastq"
,
libDir
+
sampleId
+
"-"
+
libId
+
".R2.fastq"
)
samToFastq
.
isIntermediate
=
true
qscript
.
add
(
samToFastq
)
mapping
.
input_R1
=
samToFastq
.
fastqR1
...
...
@@ -83,17 +83,17 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
val
header
=
inputSam
.
getFileHeader
.
getReadGroups
for
(
readGroup
<-
inputSam
.
getFileHeader
.
getReadGroups
)
{
if
(
readGroup
.
getSample
!=
sampleId
)
logger
.
warn
(
"Sample ID readgroup in bam file is not the same"
)
if
(
readGroup
.
getLibrary
!=
lib
rary
Id
)
logger
.
warn
(
"Library ID readgroup in bam file is not the same"
)
if
(
readGroup
.
getSample
!=
sampleId
||
readGroup
.
getLibrary
!=
lib
rary
Id
)
readGroupOke
=
false
if
(
readGroup
.
getLibrary
!=
libId
)
logger
.
warn
(
"Library ID readgroup in bam file is not the same"
)
if
(
readGroup
.
getSample
!=
sampleId
||
readGroup
.
getLibrary
!=
libId
)
readGroupOke
=
false
}
inputSam
.
close
if
(!
readGroupOke
)
{
if
(
config
(
"correct_readgroups"
,
default
=
false
))
{
logger
.
info
(
"Correcting readgroups, file:"
+
bamFile
)
val
aorrg
=
AddOrReplaceReadGroups
(
qscript
,
bamFile
,
new
File
(
libDir
+
sampleId
+
"-"
+
lib
rary
Id
+
".bam"
))
aorrg
.
RGID
=
sampleId
+
"-"
+
lib
rary
Id
aorrg
.
RGLB
=
lib
rary
Id
val
aorrg
=
AddOrReplaceReadGroups
(
qscript
,
bamFile
,
new
File
(
libDir
+
sampleId
+
"-"
+
libId
+
".bam"
))
aorrg
.
RGID
=
sampleId
+
"-"
+
libId
aorrg
.
RGLB
=
libId
aorrg
.
RGSM
=
sampleId
aorrg
.
isIntermediate
=
true
qscript
.
add
(
aorrg
)
...
...
@@ -106,7 +106,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
Some
(
bamFile
)
}
}
else
{
logger
.
error
(
"Sample: "
+
sampleId
+
": No R1 found for run: "
+
lib
rary
Id
)
logger
.
error
(
"Sample: "
+
sampleId
+
": No R1 found for run: "
+
libId
)
None
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
ad0c55bc
...
...
@@ -40,26 +40,26 @@ trait MultiSampleQScript extends BiopetQScript {
/**
* Library class with basic functions build in
* @param lib
rary
Id
* @param libId
*/
abstract
class
AbstractLibrary
(
val
lib
rary
Id
:
String
)
{
abstract
class
AbstractLibrary
(
val
libId
:
String
)
{
/** Overrules config of qscript with default sample and default library */
val
config
=
new
ConfigFunctions
(
defaultSample
=
sampleId
,
defaultLibrary
=
lib
rary
Id
)
val
config
=
new
ConfigFunctions
(
defaultSample
=
sampleId
,
defaultLibrary
=
libId
)
/** Adds the library jobs */
final
def
addAndTrackJobs
()
:
Unit
=
{
currentSample
=
Some
(
sampleId
)
currentLib
=
Some
(
lib
rary
Id
)
currentLib
=
Some
(
libId
)
addJobs
()
currentLib
=
None
currentSample
=
None
}
/** Creates a library file with given suffix */
def
createFile
(
suffix
:
String
)
:
File
=
new
File
(
libDir
,
sampleId
+
"-"
+
lib
rary
Id
+
suffix
)
def
createFile
(
suffix
:
String
)
:
File
=
new
File
(
libDir
,
sampleId
+
"-"
+
libId
+
suffix
)
/** Returns library directory */
def
libDir
=
sampleDir
+
"lib_"
+
lib
rary
Id
+
File
.
separator
def
libDir
=
sampleDir
+
"lib_"
+
libId
+
File
.
separator
/** Function that add library jobs */
protected
def
addJobs
()
...
...
@@ -95,7 +95,7 @@ trait MultiSampleQScript extends BiopetQScript {
/** function add all libraries in one call */
protected
final
def
addPerLibJobs
()
:
Unit
=
{
for
((
lib
rary
Id
,
library
)
<-
libraries
)
{
for
((
libId
,
library
)
<-
libraries
)
{
library
.
addAndTrackJobs
()
}
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
View file @
ad0c55bc
...
...
@@ -26,7 +26,7 @@ class MultisamplePipelineTemplate(val root: Configurable) extends QScript with M
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
lib
rary
Id
:
String
)
extends
AbstractLibrary
(
lib
rary
Id
)
{
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
protected
def
addJobs
()
:
Unit
=
{
// Library jobs
}
...
...
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
ad0c55bc
...
...
@@ -44,14 +44,14 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
lib
rary
Id
:
String
)
extends
AbstractLibrary
(
lib
rary
Id
)
{
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
val
mapping
=
new
Mapping
(
qscript
)
def
addJobs
()
:
Unit
=
{
if
(
config
.
contains
(
"R1"
))
{
mapping
.
input_R1
=
config
(
"R1"
)
if
(
config
.
contains
(
"R2"
))
mapping
.
input_R2
=
config
(
"R2"
)
mapping
.
lib
rary
Id
=
lib
rary
Id
mapping
.
libId
=
libId
mapping
.
sampleId
=
sampleId
mapping
.
outputDir
=
libDir
...
...
@@ -59,7 +59,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
mapping
.
biopetScript
addAll
(
mapping
.
functions
)
}
else
logger
.
error
(
"Sample: "
+
sampleId
+
": No R1 found for library: "
+
lib
rary
Id
)
}
else
logger
.
error
(
"Sample: "
+
sampleId
+
": No R1 found for library: "
+
libId
)
}
}
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
ad0c55bc
...
...
@@ -38,7 +38,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
/** Skip Clip fastq files */
var
skipClip
:
Boolean
=
config
(
"skip_clip"
,
default
=
false
)
// TODO: hide sampleId and lib
rary
Id from the command line so they do not interfere with our config values
// TODO: hide sampleId and libId from the command line so they do not interfere with our config values
/** Sample name */
@Argument
(
doc
=
"Sample ID"
,
shortName
=
"sample"
,
required
=
true
)
...
...
@@ -46,7 +46,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
/** Library name */
@Argument
(
doc
=
"Library ID"
,
shortName
=
"library"
,
required
=
true
)
var
lib
rary
Id
:
String
=
_
var
libId
:
String
=
_
var
paired
:
Boolean
=
(
input_R2
!=
null
)
var
R1_ext
:
String
=
_
...
...
@@ -65,7 +65,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
if
(
input_R1
==
null
)
throw
new
IllegalStateException
(
"Missing R1 on flexiprep module"
)
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Missing Output directory on flexiprep module"
)
if
(
sampleId
==
null
)
throw
new
IllegalStateException
(
"Missing Sample name on flexiprep module"
)
if
(
lib
rary
Id
==
null
)
throw
new
IllegalStateException
(
"Missing Library name on flexiprep module"
)
if
(
libId
==
null
)
throw
new
IllegalStateException
(
"Missing Library name on flexiprep module"
)
else
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
paired
=
(
input_R2
!=
null
)
...
...
@@ -83,7 +83,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
R2_name
=
R2_name
.
substring
(
0
,
R2_name
.
lastIndexOf
(
R2_ext
))
}
summary
.
out
=
outputDir
+
sampleId
+
"-"
+
lib
rary
Id
+
".qc.summary.json"
summary
.
out
=
outputDir
+
sampleId
+
"-"
+
libId
+
".qc.summary.json"
}
def
biopetScript
()
{
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
View file @
ad0c55bc
...
...
@@ -121,7 +121,7 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
md5Summary
()
val
summary
=
(
"samples"
:=
(
flexiprep
.
sampleId
:=
(
"libraries"
:=
(
flexiprep
.
lib
rary
Id
:=
(
(
"libraries"
:=
(
flexiprep
.
libId
:=
(
(
"flexiprep"
:=
(
(
"clipping"
:=
!
flexiprep
.
skipClip
)
->:
(
"trimming"
:=
!
flexiprep
.
skipTrim
)
->:
...
...
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
View file @
ad0c55bc
...
...
@@ -36,7 +36,7 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
lib
rary
Id
:
String
)
extends
AbstractLibrary
(
lib
rary
Id
)
{
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
def
addJobs
()
:
Unit
=
{
}
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
ad0c55bc
...
...
@@ -67,7 +67,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
protected
var
readgroupId
:
String
=
_
/** Readgroup Library */
var
lib
rary
Id
:
String
=
_
var
libId
:
String
=
_
/** Readgroup Platform */
protected
var
platform
:
String
=
config
(
"platform"
,
default
=
"illumina"
)
...
...
@@ -100,9 +100,9 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
if
(
input_R1
==
null
)
throw
new
IllegalStateException
(
"Missing FastQ R1 on mapping module"
)
paired
=
(
input_R2
!=
null
)
if
(
lib
rary
Id
==
null
)
lib
rary
Id
=
config
(
"library_id"
)
if
(
libId
==
null
)
libId
=
config
(
"library_id"
)
if
(
sampleId
==
null
)
sampleId
=
config
(
"sample_id"
)
if
(
readgroupId
==
null
&&
sampleId
!=
null
&&
lib
rary
Id
!=
null
)
readgroupId
=
sampleId
+
"-"
+
lib
rary
Id
if
(
readgroupId
==
null
&&
sampleId
!=
null
&&
libId
!=
null
)
readgroupId
=
sampleId
+
"-"
+
libId
else
if
(
readgroupId
==
null
)
readgroupId
=
config
(
"readgroup_id"
)
if
(
outputName
==
null
)
outputName
=
readgroupId
...
...
@@ -127,7 +127,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
flexiprep
.
input_R1
=
input_R1
if
(
paired
)
flexiprep
.
input_R2
=
input_R2
flexiprep
.
sampleId
=
this
.
sampleId
flexiprep
.
lib
rary
Id
=
this
.
lib
rary
Id
flexiprep
.
libId
=
this
.
libId
flexiprep
.
init
flexiprep
.
runInitialJobs
}
...
...
@@ -279,7 +279,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var
RG
:
String
=
"ID:"
+
readgroupId
+
","
RG
+=
"SM:"
+
sampleId
+
","
RG
+=
"LB:"
+
lib
rary
Id
+
","
RG
+=
"LB:"
+
libId
+
","
if
(
readgroupDescription
!=
null
)
RG
+=
"DS"
+
readgroupDescription
+
","
RG
+=
"PU:"
+
platformUnit
+
","
if
(
predictedInsertsize
.
getOrElse
(
0
)
>
0
)
RG
+=
"PI:"
+
predictedInsertsize
.
get
+
","
...
...
@@ -330,7 +330,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
addOrReplaceReadGroups
.
createIndex
=
true
addOrReplaceReadGroups
.
RGID
=
readgroupId
addOrReplaceReadGroups
.
RGLB
=
lib
rary
Id
addOrReplaceReadGroups
.
RGLB
=
libId
addOrReplaceReadGroups
.
RGPL
=
platform
addOrReplaceReadGroups
.
RGPU
=
platformUnit
addOrReplaceReadGroups
.
RGSM
=
sampleId
...
...
@@ -344,7 +344,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def
getReadGroup
()
:
String
=
{
var
RG
:
String
=
"@RG\\t"
+
"ID:"
+
readgroupId
+
"\\t"
RG
+=
"LB:"
+
lib
rary
Id
+
"\\t"
RG
+=
"LB:"
+
libId
+
"\\t"
RG
+=
"PL:"
+
platform
+
"\\t"
RG
+=
"PU:"
+
platformUnit
+
"\\t"
RG
+=
"SM:"
+
sampleId
+
"\\t"
...
...
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @
ad0c55bc
...
...
@@ -62,16 +62,16 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
lib
rary
Id
:
String
)
extends
AbstractLibrary
(
lib
rary
Id
)
{
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
val
inputFastq
:
File
=
config
(
"R1"
,
required
=
true
)
val
prefixFastq
:
File
=
createFile
(
".prefix.fastq"
)
val
flexiprep
=
new
Flexiprep
(
qscript
)
flexiprep
.
sampleId
=
sampleId
flexiprep
.
lib
rary
Id
=
lib
rary
Id
flexiprep
.
libId
=
libId
val
mapping
=
new
Mapping
(
qscript
)
mapping
.
lib
rary
Id
=
lib
rary
Id
mapping
.
libId
=
libId
mapping
.
sampleId
=
sampleId
protected
def
addJobs
()
:
Unit
=
{
...
...
@@ -96,8 +96,8 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
qscript
.
addAll
(
mapping
.
functions
)
if
(
config
(
"library_counts"
,
default
=
false
).
asBoolean
)
{
addBedtoolsCounts
(
mapping
.
finalBamFile
,
sampleId
+
"-"
+
lib
rary
Id
,
libDir
)
addTablibCounts
(
pf
.
outputFastq
,
sampleId
+
"-"
+
lib
rary
Id
,
libDir
)
addBedtoolsCounts
(
mapping
.
finalBamFile
,
sampleId
+
"-"
+
libId
,
libDir
)
addTablibCounts
(
pf
.
outputFastq
,
sampleId
+
"-"
+
libId
,
libDir
)
}
}
}
...
...
public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
View file @
ad0c55bc
...
...
@@ -124,11 +124,11 @@ class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with
// Called for each run from a sample
def runSingleLibraryJobs(lib
rary
Id: String, sampleID: String): LibraryOutput = {
def runSingleLibraryJobs(libId: String, sampleID: String): LibraryOutput = {
val libraryOutput = new LibraryOutput
val alignmentDir: String = outputDir + sampleID + "/alignment/"
val runDir: String = alignmentDir + "run_" + lib
rary
Id + "/"
val runDir: String = alignmentDir + "run_" + libId + "/"
if (config.contains("R1")) {
val mapping = new Mapping(this)
...
...
@@ -140,7 +140,7 @@ class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with
mapping.input_R1 = config("R1")
mapping.input_R2 = config("R2")
mapping.paired = (mapping.input_R2 != null)
mapping.RGLB = lib
rary
Id
mapping.RGLB = libId
mapping.RGSM = sampleID
mapping.RGPL = config("PL")
mapping.RGPU = config("PU")
...
...
@@ -154,7 +154,7 @@ class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with
// start sambamba dedup
libraryOutput.mappedBamFile = mapping.outputFiles("finalBamFile")
} else this.logger.error("Sample: " + sampleID + ": No R1 found for library: " + lib
rary
Id)
} else this.logger.error("Sample: " + sampleID + ": No R1 found for library: " + libId)
return libraryOutput
// logger.debug(outputFiles)
// return outputFiles
...
...
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