Commit 0ebc7e0a authored by pjvan_thof's avatar pjvan_thof

Adding missing output files

parent 4fee107f
...@@ -228,6 +228,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi ...@@ -228,6 +228,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
override def summaryDeps: List[File] = qcCmdR1.summaryDeps ::: qcCmdR2.summaryDeps ::: super.summaryDeps override def summaryDeps: List[File] = qcCmdR1.summaryDeps ::: qcCmdR2.summaryDeps ::: super.summaryDeps
} }
pipe.jobOutputFile = new File(outDir, ".qc_cmd.out")
pipe.deps ::= fastqcR1.output pipe.deps ::= fastqcR1.output
pipe.deps ::= fastqcR2.output pipe.deps ::= fastqcR2.output
pipe.deps ::= R1_in pipe.deps ::= R1_in
...@@ -243,6 +244,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi ...@@ -243,6 +244,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
R2 = Some(fqSync.outputFastq2) R2 = Some(fqSync.outputFastq2)
} else { } else {
qcCmdR1.nCoresRequest = Some(2) qcCmdR1.nCoresRequest = Some(2)
qcCmdR1.jobOutputFile = new File(outDir, ".qc_cmd.out")
add(qcCmdR1) add(qcCmdR1)
R1 = qcCmdR1.output R1 = qcCmdR1.output
} }
......
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