Commit 373dbb5c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Revert "Fix on fastqc jobs"

This reverts commit 5945ab1746a433f4c9c2100176934d7ee86c38a2.
parent 613343f7
......@@ -62,7 +62,7 @@ object Fastqc {
if (filename.endsWith(".gzip")) filename = filename.substring(0, filename.size - 5)
if (filename.endsWith(".fastq")) filename = filename.substring(0, filename.size - 6)
//if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
fastqcCommand.output = new File(outDir + "/" + filename + "_fastqc.zip")
fastqcCommand.jobOutputFile = new File(outDir + "/" + filename + "_fastqc.zip")
fastqcCommand.afterGraph
return fastqcCommand
}
......
......@@ -81,18 +81,16 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
addSha1sum(outputFiles("fastq_input_R1"), "sha1_R1")
if (paired) addSha1sum(outputFiles("fastq_input_R2"), "sha1_R2")
val fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
var fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
outputFiles += ("fastqc_R1" -> fastqc_R1.output)
outputFiles += ("qualtype_R1" -> getQualtype(fastqc_R1, R1_name))
outputFiles += ("contams_R1" -> getContams(fastqc_R1, R1_name))
add(fastqc_R1)
if (paired) {
val fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
var fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
outputFiles += ("fastqc_R2" -> fastqc_R2.output)
outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2, R2_name))
outputFiles += ("contams_R2" -> getContams(fastqc_R2, R2_name))
add(fastqc_R2)
}
}
......@@ -235,14 +233,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
addSha1sum(R1, "sha1_qc_R1")
if (paired) addSha1sum(R2, "sha1_qc_R2")
val fastqc_R1 = Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/")
add(fastqc_R1)
outputFiles += ("fastqc_R1_final" -> fastqc_R1.output)
if (paired) {
val fastqc_R2 = Fastqc(this, outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/")
add(fastqc_R2)
outputFiles += ("fastqc_R2_final" -> fastqc_R2.output)
}
outputFiles += ("fastqc_R1_final" -> Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/").output)
if (paired) outputFiles += ("fastqc_R2_final" -> Fastqc(this, outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/").output)
}
if (!skipSummary) {
......
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