Commit e3b3e129 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add todo's

parent 53c4ba81
......@@ -33,20 +33,26 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
def summaryFile: File = new File(outputDir, "Sage.summary.json")
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summarySettings: Map[String, Any] = Map()
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
protected def addJobs(): Unit = {}
......
......@@ -43,20 +43,26 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
def summaryFile = new File(outputDir, "GatkPipeline.summary.json")
//TODO: Add summary
def summaryFiles = Map()
//TODO: Add summary
def summarySettings = Map()
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
val mapping = new Mapping(qscript)
......
......@@ -45,20 +45,26 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
def summaryFile = new File(outputDir, "Carp.summary.json")
//TODO: Add summary
def summaryFiles = Map()
//TODO: Add summary
def summarySettings = Map()
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
val mapping = new Mapping(qscript)
......
......@@ -35,20 +35,26 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
def summaryFile: File = new File(outputDir, "Kopisu.summary.json")
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summarySettings: Map[String, Any] = Map()
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
def addJobs(): Unit = {
......
......@@ -60,20 +60,26 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
def summaryFile: File = new File(outputDir, "Sage.summary.json")
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summarySettings: Map[String, Any] = Map()
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
val inputFastq: File = config("R1")
......
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