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Commit ad0c55bc authored by bow's avatar bow
Browse files

Rename libraryId -> libId for consistency

parent daf3d591
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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(libraryId: String) extends AbstractLibrary(libraryId) {
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(libraryId: String) extends AbstractLibrary(libraryId) {
class Library(libId: String) extends AbstractLibrary(libId) {
val mapping = new Mapping(qscript)
mapping.sampleId = sampleId
mapping.libraryId = libraryId
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 + "-" + libraryId + ".R1.fastq",
libDir + sampleId + "-" + libraryId + ".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 != libraryId) logger.warn("Library ID readgroup in bam file is not the same")
if (readGroup.getSample != sampleId || readGroup.getLibrary != libraryId) 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 + "-" + libraryId + ".bam"))
aorrg.RGID = sampleId + "-" + libraryId
aorrg.RGLB = libraryId
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: " + libraryId)
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 libraryId
* @param libId
*/
abstract class AbstractLibrary(val libraryId: String) {
abstract class AbstractLibrary(val libId: String) {
/** Overrules config of qscript with default sample and default library */
val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libraryId)
val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libId)
/** Adds the library jobs */
final def addAndTrackJobs(): Unit = {
currentSample = Some(sampleId)
currentLib = Some(libraryId)
currentLib = Some(libId)
addJobs()
currentLib = None
currentSample = None
}
/** Creates a library file with given suffix */
def createFile(suffix: String): File = new File(libDir, sampleId + "-" + libraryId + suffix)
def createFile(suffix: String): File = new File(libDir, sampleId + "-" + libId + suffix)
/** Returns library directory */
def libDir = sampleDir + "lib_" + libraryId + 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 ((libraryId, 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(libraryId: String) extends AbstractLibrary(libraryId) {
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(libraryId: String) extends AbstractLibrary(libraryId) {
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.libraryId = libraryId
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: " + libraryId)
} 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 libraryId 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 libraryId: 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 (libraryId == 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 + "-" + libraryId + ".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.libraryId := (
("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(libraryId: String) extends AbstractLibrary(libraryId) {
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 libraryId: 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 (libraryId == null) libraryId = config("library_id")
if (libId == null) libId = config("library_id")
if (sampleId == null) sampleId = config("sample_id")
if (readgroupId == null && sampleId != null && libraryId != null) readgroupId = sampleId + "-" + libraryId
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.libraryId = this.libraryId
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:" + libraryId + ","
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 = libraryId
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:" + libraryId + "\\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(libraryId: String) extends AbstractLibrary(libraryId) {
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.libraryId = libraryId
flexiprep.libId = libId
val mapping = new Mapping(qscript)
mapping.libraryId = libraryId
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 + "-" + libraryId, libDir)
addTablibCounts(pf.outputFastq, sampleId + "-" + libraryId, 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(libraryId: 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_" + libraryId + "/"
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 = libraryId
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: " + libraryId)
} else this.logger.error("Sample: " + sampleID + ": No R1 found for library: " + libId)
return libraryOutput
// logger.debug(outputFiles)
// return outputFiles
......
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