Commit fdeace11 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by Wai Yi Leung
Browse files

Also change dependency for cutadept

(cherry picked from commit 6459b271)
parent c1834fcf
......@@ -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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