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biopet.biopet
Commits
1eb69dfa
Commit
1eb69dfa
authored
Apr 08, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 08, 2017
Browse files
Merge branch 'develop' into fix-BIOPET-641
parents
58575df3
261ebe2a
Changes
1
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Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
1eb69dfa
...
@@ -230,6 +230,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
...
@@ -230,6 +230,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
pipe
.
deps
::=
fastqcR2
.
output
pipe
.
deps
::=
fastqcR2
.
output
pipe
.
deps
::=
R1_in
pipe
.
deps
::=
R1_in
pipe
.
deps
::=
R2_in
.
get
pipe
.
deps
::=
R2_in
.
get
pipe
.
nCoresRequest
=
Some
(
4
)
pipe
.
isIntermediate
=
!
keepQcFastqFiles
pipe
.
isIntermediate
=
!
keepQcFastqFiles
addSummarizable
(
pipe
,
"qc_cmd"
)
addSummarizable
(
pipe
,
"qc_cmd"
)
add
(
pipe
)
add
(
pipe
)
...
@@ -239,6 +240,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
...
@@ -239,6 +240,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
R1
=
fqSync
.
outputFastq1
R1
=
fqSync
.
outputFastq1
R2
=
Some
(
fqSync
.
outputFastq2
)
R2
=
Some
(
fqSync
.
outputFastq2
)
}
else
{
}
else
{
qcCmdR1
.
nCoresRequest
=
Some
(
2
)
add
(
qcCmdR1
)
add
(
qcCmdR1
)
R1
=
qcCmdR1
.
output
R1
=
qcCmdR1
.
output
}
}
...
...
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