From dc3bc04ff09eab6a70cffac80309b1f2d73aefcc Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 Jun 2014 09:39:39 +0200
Subject: [PATCH] fixed bug on skip arguments fixed output file when input file
is not zipped skipping final seqstat and sha1sum when skipclip and skiptrim
is true
---
.../pipelines/flexiprep/Flexiprep.scala | 20 +++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 15a304f5b..af4476e95 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -30,8 +30,8 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
config = Config.mergeConfigs(globalConfig.getAsConfig("flexiprep"), globalConfig)
- skipTrim = config.getAsBoolean("skiptrim", false)
- skipClip = config.getAsBoolean("skipclip", false)
+ if (!skipTrim) skipTrim = config.getAsBoolean("skiptrim", false)
+ if (!skipClip) skipClip = config.getAsBoolean("skipclip", false)
if (input_R1 == null) throw new IllegalStateException("Missing R1 on flexiprep module")
if (outputDir == null) throw new IllegalStateException("Missing Output directory on flexiprep module")
else if (!outputDir.endsWith("/")) outputDir += "/"
@@ -39,14 +39,14 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
if (input_R1.endsWith(".gz")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gz"))
else if (input_R1.endsWith(".gzip")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gzip"))
- else R1_name = input_R1
+ else R1_name = input_R1.getName
R1_ext = R1_name.substring(R1_name.lastIndexOf("."), R1_name.size)
R1_name = R1_name.substring(0, R1_name.lastIndexOf(R1_ext))
if (paired) {
if (input_R2.endsWith(".gz")) R2_name = input_R2.getName.substring(0, input_R2.getName.lastIndexOf(".gz"))
else if (input_R2.endsWith(".gzip")) R2_name = input_R2.getName.substring(0, input_R2.getName.lastIndexOf(".gzip"))
- else R2_name = input_R2
+ else R2_name = input_R2.getName
R2_ext = R2_name.substring(R2_name.lastIndexOf("."), R2_name.size)
R2_name = R2_name.substring(0, R2_name.lastIndexOf(R2_ext))
}
@@ -202,13 +202,13 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
}
}
- addSeqstat(R1, "seqstat_qc_R1")
- if (paired) addSeqstat(R2, "seqstat_qc_R2")
-
- addSha1sum(R1, "sha1_qc_R1")
- if (paired) addSha1sum(R2, "sha1_qc_R2")
-
if (!skipTrim || !skipClip) {
+ addSeqstat(R1, "seqstat_qc_R1")
+ if (paired) addSeqstat(R2, "seqstat_qc_R2")
+
+ addSha1sum(R1, "sha1_qc_R1")
+ if (paired) addSha1sum(R2, "sha1_qc_R2")
+
outputFiles += ("fastqc_R1_final" -> runFastqc(outputFiles("output_R1"),outputDir + "/" + R1_name + ".qc.fastqc/").output)
if (paired) outputFiles += ("fastqc_R2_final" -> runFastqc(outputFiles("output_R2"),outputDir + "/" + R2_name + ".qc.fastqc/").output)
}
--
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