Commit 8f104889 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Rename function

parent 405ecae2
......@@ -34,13 +34,10 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
qscript =>
def this() = this(null)
@Input(doc = "countBed", required = false)
var countBed: File = config("count_bed")
@Input(doc = "squishedCountBed, by suppling this file the auto squish job will be skipped", required = false)
var squishedCountBed: File = config("squished_count_bed")
@Input(doc = "Transcriptome, used for generation of tag library", required = false)
var transcriptome: File = config("transcriptome")
var tagsLibrary: File = config("tags_library")
......@@ -54,9 +51,9 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
)
)
def initSample(id: String) = new Sample(id)
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def initLibrary(id: String) = new Library(id)
def makeLibrary(id: String) = new Library(id)
class Library(libraryId: String) extends AbstractLibrary(libraryId) {
val inputFastq: File = config("R1", required = true)
val prefixFastq: File = new File(getLibraryDir, sampleId + "-" + libraryId + ".prefix.fastq")
......
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