Commit 449202bd authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove queue args from pipeline

parent 8f104889
......@@ -32,16 +32,16 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
@Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", required = false)
var input_R2: File = _
@Argument(doc = "Skip Trim fastq files", shortName = "skiptrim", required = false)
var skipTrim: Boolean = config("skiptrim", default = false)
/** Skip Trim fastq files */
var skipTrim: Boolean = config("skip_trim", default = false)
@Argument(doc = "Skip Clip fastq files", shortName = "skipclip", required = false)
var skipClip: Boolean = config("skipclip", default = false)
/** Skip Clip fastq files */
var skipClip: Boolean = config("skip_clip", default = false)
@Argument(doc = "Sample name", shortName = "sample", required = true)
/** Sample name */
var sampleName: String = _
@Argument(doc = "Library name", shortName = "library", required = true)
/** Library name */
var libraryName: String = _
var paired: Boolean = (input_R2 != null)
......@@ -136,24 +136,28 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
var deps: List[File] = if (paired) List(R1, R2) else List(R1)
val seqtkSeq_R1 = SeqtkSeq(this, R1, swapExt(outDir, R1, R1_ext, ".sanger" + R1_ext), fastqc_R1)
add(seqtkSeq_R1, isIntermediate = true)
seqtkSeq_R1.isIntermediate = true
add(seqtkSeq_R1)
R1 = seqtkSeq_R1.output
deps ::= R1
if (paired) {
val seqtkSeq_R2 = SeqtkSeq(this, R2, swapExt(outDir, R2, R2_ext, ".sanger" + R2_ext), fastqc_R2)
add(seqtkSeq_R2, isIntermediate = true)
seqtkSeq_R2.isIntermediate = true
add(seqtkSeq_R2)
R2 = seqtkSeq_R2.output
deps ::= R2
}
val seqstat_R1 = Seqstat(this, R1, outDir)
add(seqstat_R1, isIntermediate = true)
seqstat_R1.isIntermediate = true
add(seqstat_R1)
summary.addSeqstat(seqstat_R1, R2 = false, after = false, chunk)
if (paired) {
val seqstat_R2 = Seqstat(this, R2, outDir)
add(seqstat_R2, isIntermediate = true)
seqstat_R2.isIntermediate = true
add(seqstat_R2)
summary.addSeqstat(seqstat_R2, R2 = true, after = false, chunk)
}
......@@ -161,7 +165,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val cutadapt_R1 = Cutadapt(this, R1, swapExt(outDir, R1, R1_ext, ".clip" + R1_ext))
cutadapt_R1.fastqc = fastqc_R1
add(cutadapt_R1, isIntermediate = true)
cutadapt_R1.isIntermediate = true
add(cutadapt_R1)
summary.addCutadapt(cutadapt_R1, R2 = false, chunk)
R1 = cutadapt_R1.fastq_output
deps ::= R1
......@@ -171,7 +176,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val cutadapt_R2 = Cutadapt(this, R2, swapExt(outDir, R2, R2_ext, ".clip" + R2_ext))
outputFiles += ("cutadapt_R2_stats" -> cutadapt_R2.stats_output)
cutadapt_R2.fastqc = fastqc_R2
add(cutadapt_R2, isIntermediate = true)
cutadapt_R2.isIntermediate = true
add(cutadapt_R2)
summary.addCutadapt(cutadapt_R2, R2 = true, chunk)
R2 = cutadapt_R2.fastq_output
deps ::= R2
......@@ -179,7 +185,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val fastqSync = FastqSync(this, cutadapt_R1.fastq_input, cutadapt_R1.fastq_output, cutadapt_R2.fastq_output,
swapExt(outDir, R1, R1_ext, ".sync" + R1_ext), swapExt(outDir, R2, R2_ext, ".sync" + R2_ext), swapExt(outDir, R1, R1_ext, ".sync.stats"))
fastqSync.deps :::= deps
add(fastqSync, isIntermediate = true)
fastqSync.isIntermediate = true
add(fastqSync)
summary.addFastqcSync(fastqSync, chunk)
outputFiles += ("syncStats" -> fastqSync.output_stats)
R1 = fastqSync.output_R1
......
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