From fdeace11ddf6826ce3b4cff4df467b0479b83e75 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 19 Mar 2015 12:17:08 +0100
Subject: [PATCH] Also change dependency for cutadept (cherry picked from
commit 6459b27)
---
.../pipelines/flexiprep/Flexiprep.scala | 25 +++++++++++--------
1 file changed, 15 insertions(+), 10 deletions(-)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index ef830c57a..c7459f78f 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -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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