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Commit f60b77cc authored by Peter van 't Hof's avatar Peter van 't Hof
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Remove Queue command args

parent 449202bd
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public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+ 66
− 67
View file @ f60b77cc
......@@ -38,60 +38,59 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
@Input(doc = "R2 fastq file", shortName = "R2", required = false)
var input_R2: File = _
@Argument(doc = "Output name", shortName = "outputName", required = false)
/** Output name */
var outputName: String = _
@Argument(doc = "Skip flexiprep", shortName = "skipflexiprep", required = false)
var skipFlexiprep: Boolean = false
/** Skip flexiprep */
protected var skipFlexiprep: Boolean = config("skip_flexiprep", default = false)
@Argument(doc = "Skip mark duplicates", shortName = "skipmarkduplicates", required = false)
var skipMarkduplicates: Boolean = false
/** Skip mark duplicates */
protected var skipMarkduplicates: Boolean = config("skip_markduplicates", default = false)
@Argument(doc = "Skip metrics", shortName = "skipmetrics", required = false)
var skipMetrics: Boolean = false
/** Skip metrics */
protected var skipMetrics: Boolean = config("skip_metrics", default = false)
@Argument(doc = "Aligner", shortName = "ALN", required = false)
var aligner: String = config("aligner", default = "bwa")
/** Aligner */
protected var aligner: String = config("aligner", default = "bwa")
@Argument(doc = "Reference", shortName = "R", required = false)
var reference: File = config("reference")
/** Reference */
protected var reference: File = config("reference")
@Argument(doc = "Chunking", shortName = "chunking", required = false)
var chunking: Boolean = config("chunking", false)
/** Number of chunks, when not defined pipeline will automatic calculate number of chunks */
protected var numberChunks: Option[Int] = config("number_chunks")
@ClassType(classOf[Int])
@Argument(doc = "Number of chunks, when not defined pipeline will automatic calculate number of chunks", shortName = "numberChunks", required = false)
var numberChunks: Option[Int] = None
/** Enable chunking */
protected var chunking: Boolean = config("chunking", numberChunks.getOrElse(1) > 1)
// Readgroup items
@Argument(doc = "Readgroup ID", shortName = "RGID", required = false)
var RGID: String = config("RGID")
/** Readgroup ID */
protected var readgroupId: String = _
@Argument(doc = "Readgroup Library", shortName = "RGLB", required = false)
var RGLB: String = config("RGLB")
/** Readgroup Library */
var libraryId: String = _
@Argument(doc = "Readgroup Platform", shortName = "RGPL", required = false)
var RGPL: String = config("RGPL", default = "illumina")
/** Readgroup Platform */
protected var platform: String = config("platform", default = "illumina")
@Argument(doc = "Readgroup platform unit", shortName = "RGPU", required = false)
var RGPU: String = config("RGPU", default = "na")
/** Readgroup platform unit */
protected var platformUnit: String = config("platform_unit", default = "na")
@Argument(doc = "Readgroup sample", shortName = "RGSM", required = false)
var RGSM: String = config("RGSM")
/**Readgroup sample */
var sampleId: String = _
@Argument(doc = "Readgroup sequencing center", shortName = "RGCN", required = false)
var RGCN: String = config("RGCN")
/** Readgroup sequencing center */
protected var readgroupSequencingCenter: Option[String] = config("readgroup_sequencing_center")
@Argument(doc = "Readgroup description", shortName = "RGDS", required = false)
var RGDS: String = config("RGDS")
/** Readgroup description */
protected var readgroupDescription: Option[String] = config("readgroup_description")
@Argument(doc = "Readgroup sequencing date", shortName = "RGDT", required = false)
var RGDT: Date = _
/** Readgroup sequencing date */
protected var readgroupDate: Date = _
@Argument(doc = "Readgroup predicted insert size", shortName = "RGPI", required = false)
var RGPI: Option[Int] = config("RGPI")
/** Readgroup predicted insert size */
protected var predictedInsertsize: Option[Int] = config("predicted_insertsize")
var paired: Boolean = false
protected var paired: Boolean = false
val flexiprep = new Flexiprep(this)
def init() {
......@@ -100,12 +99,12 @@ 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 (RGLB == null) throw new IllegalStateException("Missing Readgroup library on mapping module")
if (RGLB == null) throw new IllegalStateException("Missing Readgroup sample on mapping module")
if (RGID == null && RGSM != null && RGLB != null) RGID = RGSM + "-" + RGLB
else if (RGID == null) throw new IllegalStateException("Missing Readgroup ID on mapping module")
if (libraryId == null) libraryId = config("library_id")
if (sampleId == null) sampleId = config("sample_id")
if (readgroupId == null && sampleId != null && libraryId != null) readgroupId = sampleId + "-" + libraryId
else if (readgroupId == null) readgroupId = config("readgroup_id")
if (outputName == null) outputName = RGID
if (outputName == null) outputName = readgroupId
if (chunking) {
if (numberChunks.isEmpty) {
......@@ -126,8 +125,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
flexiprep.outputDir = outputDir + "flexiprep/"
flexiprep.input_R1 = input_R1
if (paired) flexiprep.input_R2 = input_R2
flexiprep.sampleName = this.RGSM
flexiprep.libraryName = this.RGLB
flexiprep.sampleName = this.sampleId
flexiprep.libraryName = this.libraryId
flexiprep.init
flexiprep.runInitialJobs
}
......@@ -275,15 +274,15 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def addStampy(R1: File, R2: File, output: File, deps: List[File]): File = {
var RG: String = "ID:" + RGID + ","
RG += "SM:" + RGSM + ","
RG += "LB:" + RGLB + ","
if (RGDS != null) RG += "DS" + RGDS + ","
RG += "PU:" + RGPU + ","
if (RGPI > 0) RG += "PI:" + RGPI + ","
if (RGCN != null) RG += "CN:" + RGCN + ","
if (RGDT != null) RG += "DT:" + RGDT + ","
RG += "PL:" + RGPL
var RG: String = "ID:" + readgroupId + ","
RG += "SM:" + sampleId + ","
RG += "LB:" + libraryId + ","
if (readgroupDescription != null) RG += "DS" + readgroupDescription + ","
RG += "PU:" + platformUnit + ","
if (predictedInsertsize.getOrElse(0) > 0) RG += "PI:" + predictedInsertsize.get + ","
if (readgroupSequencingCenter.isDefined) RG += "CN:" + readgroupSequencingCenter.get + ","
if (readgroupDate != null) RG += "DT:" + readgroupDate + ","
RG += "PL:" + platform
val stampyCmd = new Stampy(this)
stampyCmd.R1 = R1
......@@ -327,13 +326,13 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
val addOrReplaceReadGroups = AddOrReplaceReadGroups(this, input, output)
addOrReplaceReadGroups.createIndex = true
addOrReplaceReadGroups.RGID = RGID
addOrReplaceReadGroups.RGLB = RGLB
addOrReplaceReadGroups.RGPL = RGPL
addOrReplaceReadGroups.RGPU = RGPU
addOrReplaceReadGroups.RGSM = RGSM
if (RGCN != null) addOrReplaceReadGroups.RGCN = RGCN
if (RGDS != null) addOrReplaceReadGroups.RGDS = RGDS
addOrReplaceReadGroups.RGID = readgroupId
addOrReplaceReadGroups.RGLB = libraryId
addOrReplaceReadGroups.RGPL = platform
addOrReplaceReadGroups.RGPU = platformUnit
addOrReplaceReadGroups.RGSM = sampleId
if (readgroupSequencingCenter.isDefined) addOrReplaceReadGroups.RGCN = readgroupSequencingCenter.get
if (readgroupDescription.isDefined) addOrReplaceReadGroups.RGDS = readgroupDescription.get
if (!skipMarkduplicates) addOrReplaceReadGroups.isIntermediate = true
add(addOrReplaceReadGroups)
......@@ -341,15 +340,15 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
}
def getReadGroup(): String = {
var RG: String = "@RG\\t" + "ID:" + RGID + "\\t"
RG += "LB:" + RGLB + "\\t"
RG += "PL:" + RGPL + "\\t"
RG += "PU:" + RGPU + "\\t"
RG += "SM:" + RGSM + "\\t"
if (RGCN != null) RG += "CN:" + RGCN + "\\t"
if (RGDS != null) RG += "DS" + RGDS + "\\t"
if (RGDT != null) RG += "DT" + RGDT + "\\t"
if (RGPI.isDefined) RG += "PI" + RGPI.get + "\\t"
var RG: String = "@RG\\t" + "ID:" + readgroupId + "\\t"
RG += "LB:" + libraryId + "\\t"
RG += "PL:" + platform + "\\t"
RG += "PU:" + platformUnit + "\\t"
RG += "SM:" + sampleId + "\\t"
if (readgroupSequencingCenter.isDefined) RG += "CN:" + readgroupSequencingCenter.get + "\\t"
if (readgroupDescription.isDefined) RG += "DS" + readgroupDescription.get + "\\t"
if (readgroupDate != null) RG += "DT" + readgroupDate + "\\t"
if (predictedInsertsize.isDefined) RG += "PI" + predictedInsertsize.get + "\\t"
return RG.substring(0, RG.lastIndexOf("\\t"))
}
......
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