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biopet.biopet
Commits
d107727c
Commit
d107727c
authored
Nov 29, 2015
by
Peter van 't Hof
Browse files
Fix graph issues
parent
6cb4dcbe
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
d107727c
...
...
@@ -195,6 +195,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
override
def
beforeGraph
()
:
Unit
=
{
fqSync
.
beforeGraph
()
commands
=
qcCmdR1
.
jobs
:::
qcCmdR2
.
jobs
:::
fqSync
::
Nil
super
.
beforeGraph
()
}
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
d107727c
...
...
@@ -50,7 +50,15 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
val
seqtk
=
new
SeqtkSeq
(
root
)
var
clip
:
Option
[
Cutadapt
]
=
None
var
trim
:
Option
[
Sickle
]
=
None
var
outputCommand
:
BiopetCommandLineFunction
=
null
lazy
val
outputCommand
:
BiopetCommandLineFunction
=
if
(
compress
)
{
val
gzip
=
Gzip
(
root
)
gzip
.
output
=
output
gzip
}
else
{
val
cat
=
Cat
(
root
)
cat
.
output
=
output
cat
}
def
jobs
=
(
Some
(
seqtk
)
::
clip
::
trim
::
Some
(
outputCommand
)
::
Nil
).
flatten
...
...
@@ -123,16 +131,9 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
case
_
=>
seqtk
.
output
}
if
(
compress
)
outputCommand
=
{
val
gzip
=
new
Gzip
(
root
)
gzip
.
output
=
output
outputFile
:<:
gzip
}
else
outputCommand
=
{
val
cat
=
new
Cat
(
root
)
cat
.
input
=
outputFile
::
Nil
cat
.
output
=
output
cat
outputCommand
match
{
case
gzip
:
Gzip
=>
outputFile
:<:
gzip
case
cat
:
Cat
=>
cat
.
input
=
outputFile
::
Nil
}
seqtk
.
beforeGraph
()
...
...
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