Commit 3c83721a authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding input files to check

parent 37b9a6d3
......@@ -85,6 +85,9 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
paired = input_R2.isDefined
inputFiles :+= InputFile(input_R1)
input_R2.foreach(inputFiles :+= InputFile(_))
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"))
else R1_name = input_R1.getName
......
......@@ -137,6 +137,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
require(sampleId.isDefined, "Missing sample ID on mapping module")
require(libId.isDefined, "Missing library ID on mapping module")
inputFiles :+= InputFile(input_R1)
input_R2.foreach(inputFiles :+= InputFile(_))
paired = input_R2.isDefined
if (readgroupId == null) readgroupId = sampleId.get + "-" + libId.get
......
......@@ -136,8 +136,12 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
case (true, _) => mapping.foreach(mapping => {
mapping.input_R1 = config("R1")
mapping.input_R2 = config("R2")
inputFiles :+= InputFile(mapping.input_R1, config("R1_md5"))
mapping.input_R2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
})
case (false, true) => config("bam_to_fastq", default = false).asBoolean match {
case (false, true) => {
inputFiles :+= InputFile(config("bam"), config("bam_md5"))
config("bam_to_fastq", default = false).asBoolean match {
case true =>
val samToFastq = SamToFastq(qscript, config("bam"),
new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
......@@ -182,6 +186,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
add(bamLn)
}
}
}
case _ => logger.warn("Sample: " + sampleId + " Library: " + libId + ", no reads found")
}
......
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