Commit 24a1b29e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing Biopet-493

parent 725ed53a
...@@ -204,7 +204,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with ...@@ -204,7 +204,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
fqSync.outputFastq2 = new File(outDir, fastqR2Qc.get.getName) fqSync.outputFastq2 = new File(outDir, fastqR2Qc.get.getName)
fqSync.outputStats = new File(outDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.sync.stats") fqSync.outputStats = new File(outDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.sync.stats")
val pipe = new BiopetFifoPipe(this, fqSync :: Nil) with Summarizable { val pipe = new BiopetFifoPipe(this, fqSync :: qcCmdR1.jobs ::: qcCmdR2.jobs) with Summarizable {
override def configNamespace = "qc_cmd" override def configNamespace = "qc_cmd"
override def beforeGraph(): Unit = { override def beforeGraph(): Unit = {
...@@ -233,6 +233,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with ...@@ -233,6 +233,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
pipe.deps ::= fastqcR1.output pipe.deps ::= fastqcR1.output
pipe.deps ::= fastqcR2.output pipe.deps ::= fastqcR2.output
pipe.deps ::= R1_in
pipe.deps ::= R2_in.get
pipe.isIntermediate = !keepQcFastqFiles pipe.isIntermediate = !keepQcFastqFiles
addSummarizable(pipe, "qc_cmd") addSummarizable(pipe, "qc_cmd")
add(pipe) add(pipe)
......
...@@ -171,7 +171,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S ...@@ -171,7 +171,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val chunkSize: String = config("chunksize", default = "5G") val chunkSize: String = config("chunksize", default = "5G")
val filesize = if (inputR1.getName.endsWith(".gz") || inputR1.getName.endsWith(".gzip")) inputR1.length * 3 val filesize = if (inputR1.getName.endsWith(".gz") || inputR1.getName.endsWith(".gzip")) inputR1.length * 3
else inputR1.length else inputR1.length
numberChunks = Option(ceil(filesize.toDouble / textToSize(chunkSize)).toInt) numberChunks = Some(ceil(filesize.toDouble / textToSize(chunkSize)).toInt)
if (numberChunks == Some(0)) numberChunks = Some(1)
} }
} }
logger.debug("Chunks: " + numberChunks.getOrElse(1)) logger.debug("Chunks: " + numberChunks.getOrElse(1))
......
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