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biopet.biopet
Commits
207613f6
Commit
207613f6
authored
Feb 17, 2016
by
Peter van 't Hof
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Added check to output files of flexiprep also
parent
3f86deaf
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public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+11
-0
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public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
207613f6
...
...
@@ -265,6 +265,17 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
}
}
val
validateFastq
=
new
ValidateFastq
(
this
)
validateFastq
.
r1Fastq
=
fastqR1Qc
validateFastq
.
r2Fastq
=
fastqR2Qc
validateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".validate_fastq.qc.log.out"
)
add
(
validateFastq
)
val
checkValidateFastq
=
new
CheckValidateFastq
checkValidateFastq
.
inputLogFile
=
validateFastq
.
jobOutputFile
checkValidateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".check.validate_fastq.qc.log.out"
)
add
(
checkValidateFastq
)
outputFiles
+=
(
"output_R1_gzip"
->
fastqR1Qc
)
if
(
paired
)
outputFiles
+=
(
"output_R2_gzip"
->
fastqR2Qc
.
get
)
...
...
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