Commit e04af32c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added option to skip abort step

parent b4025176
......@@ -120,10 +120,12 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
validateFastq.jobOutputFile = new File(outputDir, ".validate_fastq.log.out")
add(validateFastq)
val checkValidateFastq = new CheckValidateFastq
checkValidateFastq.inputLogFile = validateFastq.jobOutputFile
checkValidateFastq.jobOutputFile = new File(outputDir, ".check.validate_fastq.log.out")
add(checkValidateFastq)
if (config("abort_on_corrupt_fastq", default = true)) {
val checkValidateFastq = new CheckValidateFastq
checkValidateFastq.inputLogFile = validateFastq.jobOutputFile
checkValidateFastq.jobOutputFile = new File(outputDir, ".check.validate_fastq.log.out")
add(checkValidateFastq)
}
if (paired) {
fastqc_R2 = Fastqc(this, input_R2.get, new File(outputDir, R2_name + ".fastqc/"))
......@@ -271,10 +273,12 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
validateFastq.jobOutputFile = new File(outputDir, ".validate_fastq.qc.log.out")
add(validateFastq)
val checkValidateFastq = new CheckValidateFastq
checkValidateFastq.inputLogFile = validateFastq.jobOutputFile
checkValidateFastq.jobOutputFile = new File(outputDir, ".check.validate_fastq.qc.log.out")
add(checkValidateFastq)
if (config("abort_on_corrupt_fastq", default = true)) {
val checkValidateFastq = new CheckValidateFastq
checkValidateFastq.inputLogFile = validateFastq.jobOutputFile
checkValidateFastq.jobOutputFile = new File(outputDir, ".check.validate_fastq.qc.log.out")
add(checkValidateFastq)
}
outputFiles += ("output_R1_gzip" -> fastqR1Qc)
if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get)
......
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