Commit 85f7eb91 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Always execute fastqc_qc

parent 2d241e33
...@@ -250,24 +250,22 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with ...@@ -250,24 +250,22 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
if (fastq_R1.length != fastq_R2.length && paired) if (fastq_R1.length != fastq_R2.length && paired)
throw new IllegalStateException("R1 and R2 file number is not the same") throw new IllegalStateException("R1 and R2 file number is not the same")
if (!skipTrim || !skipClip) { if (fastq_R1.length > 1) {
if (fastq_R1.length > 1) { add(Zcat(this, fastq_R1, fastqR1Qc) | new Gzip(this) > fastqR1Qc)
add(Zcat(this, fastq_R1, fastqR1Qc) | new Gzip(this) > fastqR1Qc) if (paired) add(Zcat(this, fastq_R2, fastqR2Qc.get) | new Gzip(this) > fastqR2Qc.get)
if (paired) add(Zcat(this, fastq_R2, fastqR2Qc.get) | new Gzip(this) > fastqR2Qc.get) }
}
outputFiles += ("output_R1_gzip" -> fastqR1Qc) outputFiles += ("output_R1_gzip" -> fastqR1Qc)
if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get) if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get)
fastqc_R1_after = Fastqc(this, fastqR1Qc, new File(outputDir, R1_name + ".qc.fastqc/")) fastqc_R1_after = Fastqc(this, fastqR1Qc, new File(outputDir, R1_name + ".qc.fastqc/"))
add(fastqc_R1_after) add(fastqc_R1_after)
addSummarizable(fastqc_R1_after, "fastqc_R1_qc") addSummarizable(fastqc_R1_after, "fastqc_R1_qc")
if (paired) { if (paired) {
fastqc_R2_after = Fastqc(this, fastqR2Qc.get, new File(outputDir, R2_name + ".qc.fastqc/")) fastqc_R2_after = Fastqc(this, fastqR2Qc.get, new File(outputDir, R2_name + ".qc.fastqc/"))
add(fastqc_R2_after) add(fastqc_R2_after)
addSummarizable(fastqc_R2_after, "fastqc_R2_qc") addSummarizable(fastqc_R2_after, "fastqc_R2_qc")
}
} }
addSummaryJobs() addSummaryJobs()
......
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