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biopet.biopet
Commits
0ebc7e0a
Commit
0ebc7e0a
authored
Apr 20, 2017
by
pjvan_thof
Browse files
Adding missing output files
parent
4fee107f
Changes
1
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Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
0ebc7e0a
...
...
@@ -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
}
pipe
.
jobOutputFile
=
new
File
(
outDir
,
".qc_cmd.out"
)
pipe
.
deps
::=
fastqcR1
.
output
pipe
.
deps
::=
fastqcR2
.
output
pipe
.
deps
::=
R1_in
...
...
@@ -243,6 +244,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
R2
=
Some
(
fqSync
.
outputFastq2
)
}
else
{
qcCmdR1
.
nCoresRequest
=
Some
(
2
)
qcCmdR1
.
jobOutputFile
=
new
File
(
outDir
,
".qc_cmd.out"
)
add
(
qcCmdR1
)
R1
=
qcCmdR1
.
output
}
...
...
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