diff --git a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
index f71dfefb75ea9cd38ed2415161d1e794ec9ae755..5088e44c2eca6f54b23104c7695c3a03d5f762c8 100644
--- a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+++ b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
@@ -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 = {}
}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index 0c88447906c21a55a1e398a3c8c4786f18bebbf1..c76139133f23cf434884ad69ccc9dafc69b2cac9 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -42,10 +42,10 @@ 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 */
@@ -66,8 +66,8 @@ 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
@@ -82,17 +82,17 @@ 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)
@@ -105,7 +105,7 @@ 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
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index 0217615d1bedf61bdac37f878f7f1fcdf698b0ec..eb76502c8593a9e970ea2c95b9152569dfffb389 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -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()
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
index 271c06085ddd086a5f015c88d84e29a008272c89..7d46c4b8fb910398f61e9fb3b873f682efaf023f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
@@ -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
}
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index f0ff3f4eb54cc109ebe2e2b7bb7659cc99b7c76b..578f3afc79f6cac8d2621399bb577222383ee2bb 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -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)
}
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 42ea3b6d9d9f407476d359268b5ac3c40798b745..98daba52d0960fa63b4f33b43117c3fb456bddc4 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -38,13 +38,17 @@ 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 libId from the command line so they do not interfere with our config values
+
/** Sample name */
+ @Argument(doc = "Sample ID", shortName = "sample", required = true)
var sampleId: String = _
/** Library name */
- var libraryId: String = _
+ @Argument(doc = "Library ID", shortName = "library", required = true)
+ var libId: String = _
- var paired: Boolean = (input_R2 != null)
+ var paired: Boolean = input_R2.isDefined
var R1_ext: String = _
var R2_ext: String = _
var R1_name: String = _
@@ -58,11 +62,12 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val summary = new FlexiprepSummary(this)
def init() {
- 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")
- else if (!outputDir.endsWith("/")) outputDir += "/"
+ require(outputDir != null, "Missing output directory on flexiprep module")
+ require(input_R1 != null, "Missing input R1 on flexiprep module")
+ require(sampleId != null, "Missing sample ID on flexiprep module")
+ require(libId != null, "Missing library ID on flexiprep module")
+
+ paired = input_R2.isDefined
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"))
@@ -82,7 +87,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
case _ =>
}
- summary.out = outputDir + sampleId + "-" + libraryId + ".qc.summary.json"
+ summary.out = outputDir + sampleId + "-" + libId + ".qc.summary.json"
}
def biopetScript() {
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
index 84acd18206b1f44e37e60b7c6d3b703e1b0d2d21..353fb1acb83c75fe121d064c1ab6b0149f87565d 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
@@ -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) ->:
diff --git a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
index 5360b4ac78824c2e26649a12e1cc3c35262a8b50..94b3bcbe619ee5b01bd29bea6aa9b9e707934a6d 100644
--- a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
+++ b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
@@ -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 = {
}
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 74779fc20935b6163dceb4f1c3ab57cda0c34c80..9094d38cddbe70d8c7b6787200d2afe94e19d486 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -66,8 +66,15 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
/** Readgroup ID */
protected var readgroupId: String = _
+ // TODO: hide sampleId and libId from the command line so they do not interfere with our config values
+
/** Readgroup Library */
- var libraryId: String = _
+ @Argument(doc = "Library ID", shortName = "library", required = true)
+ var libId: String = _
+
+ /**Readgroup sample */
+ @Argument(doc = "Sample ID", shortName = "sample", required = true)
+ var sampleId: String = _
/** Readgroup Platform */
protected var platform: String = config("platform", default = "illumina")
@@ -75,9 +82,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
/** Readgroup platform unit */
protected var platformUnit: String = config("platform_unit", default = "na")
- /**Readgroup sample */
- var sampleId: String = _
-
/** Readgroup sequencing center */
protected var readgroupSequencingCenter: Option[String] = config("readgroup_sequencing_center")
@@ -95,14 +99,14 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def finalBamFile: File = outputDir + outputName + ".final.bam"
def init() {
- if (outputDir == null) throw new IllegalStateException("Missing Output directory on mapping module")
- else if (!outputDir.endsWith("/")) outputDir += "/"
- if (input_R1 == null) throw new IllegalStateException("Missing FastQ R1 on mapping module")
+ require(outputDir != null, "Missing output directory on mapping module")
+ require(input_R1 != null, "Missing output directory on mapping module")
+ require(sampleId != null, "Missing sample ID on mapping module")
+ require(libId != null, "Missing library ID on mapping module")
+
paired = input_R2.isDefined
- if (libraryId == null) libraryId = 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 +131,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
flexiprep.input_R1 = input_R1
flexiprep.input_R2 = input_R2
flexiprep.sampleId = this.sampleId
- flexiprep.libraryId = this.libraryId
+ flexiprep.libId = this.libId
flexiprep.init
flexiprep.runInitialJobs
}
@@ -281,7 +285,7 @@ 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 + ","
@@ -332,7 +336,7 @@ 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
@@ -346,7 +350,7 @@ 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"
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index e51be1d7164bd1234f831418e7c1eedaca2f7235..ed55ca382d13346b3cbb7bb4862941ef4da591f5 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -59,16 +59,16 @@ 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 = {
@@ -93,8 +93,8 @@ 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)
}
}
}
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index 8e3ef0af511f28b19dda8403258b024ab8936b42..206c92a69453105fb2034d6cd72cce00f5ab75cd 100644
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -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