Commit 6459b271 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Also change dependency for cutadept

parent 95db7a53
......@@ -166,14 +166,16 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
var R1: File = new File(R1_in)
var R2: File = if (paired) new File(R2_in) else null
var deps: List[File] = if (paired) List(R1, R2) else List(R1)
var deps_R1: List[File] = R1 :: Nil
var deps_R2: List[File] = if (paired) R2 :: Nil else Nil
def deps: List[File] = deps_R1 ::: deps_R2
val seqtkSeq_R1 = SeqtkSeq(this, R1, swapExt(outDir, R1, R1_ext, ".sanger" + R1_ext), fastqc_R1)
seqtkSeq_R1.isIntermediate = true
add(seqtkSeq_R1)
addSummarizable(seqtkSeq_R1, "seqtkSeq_R1")
R1 = seqtkSeq_R1.output
deps ::= R1
deps_R1 ::= R1
if (paired) {
val seqtkSeq_R2 = SeqtkSeq(this, R2, swapExt(outDir, R2, R2_ext, ".sanger" + R2_ext), fastqc_R2)
......@@ -181,19 +183,19 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
add(seqtkSeq_R2)
addSummarizable(seqtkSeq_R2, "seqtkSeq_R2")
R2 = seqtkSeq_R2.output
deps ::= R2
deps_R2 ::= R2
}
val seqstat_R1 = Seqstat(this, R1, outDir)
seqstat_R1.isIntermediate = true
seqstat_R1.deps = deps
seqstat_R1.deps = deps_R1
add(seqstat_R1)
addSummarizable(seqstat_R1, "seqstat_R1")
if (paired) {
val seqstat_R2 = Seqstat(this, R2, outDir)
seqstat_R2.isIntermediate = true
seqstat_R2.deps = deps
seqstat_R2.deps = deps_R2
add(seqstat_R2)
addSummarizable(seqstat_R2, "seqstat_R2")
}
......@@ -203,10 +205,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val cutadapt_R1 = Cutadapt(this, R1, swapExt(outDir, R1, R1_ext, ".clip" + R1_ext))
cutadapt_R1.fastqc = fastqc_R1
cutadapt_R1.isIntermediate = true
cutadapt_R1.deps = deps_R1
add(cutadapt_R1)
addSummarizable(cutadapt_R1, "clipping_R1")
R1 = cutadapt_R1.fastq_output
deps ::= R1
deps_R1 ::= R1
outputFiles += ("cutadapt_R1_stats" -> cutadapt_R1.stats_output)
if (paired) {
......@@ -214,10 +217,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
outputFiles += ("cutadapt_R2_stats" -> cutadapt_R2.stats_output)
cutadapt_R2.fastqc = fastqc_R2
cutadapt_R2.isIntermediate = true
cutadapt_R2.deps = deps_R2
add(cutadapt_R2)
addSummarizable(cutadapt_R2, "clipping_R2")
R2 = cutadapt_R2.fastq_output
deps ::= R2
deps_R2 ::= R2
val fqSync = new FastqSync(this)
fqSync.refFastq = cutadapt_R1.fastq_input
......@@ -232,7 +236,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
outputFiles += ("syncStats" -> fqSync.outputStats)
R1 = fqSync.outputFastq1
R2 = fqSync.outputFastq2
deps :::= R1 :: R2 :: Nil
deps_R1 ::= R1
deps_R2 ::= R2
}
}
......@@ -255,13 +260,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
}
val seqstat_R1_after = Seqstat(this, R1, outDir)
seqstat_R1_after.deps = deps
seqstat_R1_after.deps = deps_R1
add(seqstat_R1_after)
addSummarizable(seqstat_R1_after, "seqstat_R1_after")
if (paired) {
val seqstat_R2_after = Seqstat(this, R2, outDir)
seqstat_R2_after.deps = deps
seqstat_R2_after.deps = deps_R2
add(seqstat_R2_after)
addSummarizable(seqstat_R2_after, "seqstat_R2_after")
}
......
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