Commit d4e45996 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added a option to not keep the last fastq file anymore

parent 0ae99234
......@@ -37,6 +37,9 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Skip Clip fastq files */
var skipClip: Boolean = config("skip_clip", default = false)
/** Make a final fastq files, by default only when flexiprep is the main pipeline */
var keepQcFastqFiles: Boolean = config("keepQcFastqFiles", default = root == null)
/** Location of summary file */
def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".qc.summary.json")
......@@ -264,13 +267,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val R1 = new File(outputDir, R1_name + ".qc" + R1_ext + ".gz")
val R2 = new File(outputDir, R2_name + ".qc" + R2_ext + ".gz")
add(Gzip(this, fastq_R1, R1))
if (paired) add(Gzip(this, fastq_R2, R2))
if (!skipTrim || !skipClip) {
add(Gzip(this, fastq_R1, R1), !keepQcFastqFiles)
if (paired) add(Gzip(this, fastq_R2, R2), !keepQcFastqFiles)
outputFiles += ("output_R1_gzip" -> R1)
if (paired) outputFiles += ("output_R2_gzip" -> R2)
outputFiles += ("output_R1_gzip" -> R1)
if (paired) outputFiles += ("output_R2_gzip" -> R2)
if (!skipTrim || !skipClip) {
fastqc_R1_after = Fastqc(this, R1, new File(outputDir, R1_name + ".qc.fastqc/"))
add(fastqc_R1_after)
addSummarizable(fastqc_R1_after, "fastqc_R1_qc")
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment