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biopet.biopet
Commits
7a3bf3b2
Commit
7a3bf3b2
authored
Sep 25, 2015
by
Peter van 't Hof
Browse files
Fixed QcCommand
parent
36fd8269
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
7a3bf3b2
...
...
@@ -180,17 +180,20 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val
qcCmdR1
=
new
QcCommand
(
this
,
fastqc_R1
)
qcCmdR1
.
input
=
R1_in
qcCmdR1
.
read
=
"R1"
qcCmdR1
.
output
=
if
(
paired
)
new
File
(
"/dev/stdout"
)
else
new
File
(
outDir
,
s
"${sampleId.getOrElse("
x
")}-${libId.getOrElse("
x
")}.R1.qc.fq.gz"
)
qcCmdR1
.
isIntermediate
=
paired
||
!
keepQcFastqFiles
//add(qcCmdR1)
if
(
paired
)
{
val
qcCmdR2
=
new
QcCommand
(
this
,
fastqc_R2
)
qcCmdR2
.
input
=
R2_in
.
get
qcCmdR2
.
output
=
new
File
(
"/dev/stdout"
)
//add(qcCmdR2)
qcCmdR2
.
read
=
"R2"
qcCmdR1
.
compress
=
false
qcCmdR2
.
compress
=
false
val
fqSync
=
new
FastqSync
(
this
)
fqSync
.
refFastq
=
R1_in
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
7a3bf3b2
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
BiopetPipe
}
import
nl.lumc.sasc.biopet.extensions.
{
Gzip
,
Sickle
,
Cutadapt
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Gzip
,
Sickle
,
Cutadapt
}
import
nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
...
...
@@ -24,8 +24,13 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
@Output
(
required
=
true
)
var
output
:
File
=
_
var
compress
=
true
var
read
:
String
=
_
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
require
(
read
!=
null
)
deps
:::=
fastqc
.
outputFiles
}
...
...
@@ -49,7 +54,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
val
foundAdapters
=
fastqc
.
foundAdapters
.
map
(
_
.
seq
)
if
(
foundAdapters
.
nonEmpty
)
{
val
cutadept
=
new
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
Cutadapt
(
root
)
cutadept
.
stats_output
=
new
File
(
flexiprep
.
outputDir
,
s
"${flexiprep.sampleId.getOrElse("
x
")}-${flexiprep.libId.getOrElse("
x
")}.clip.stats"
)
cutadept
.
stats_output
=
new
File
(
flexiprep
.
outputDir
,
s
"${flexiprep.sampleId.getOrElse("
x
")}-${flexiprep.libId.getOrElse("
x
")}.
$read.
clip.stats"
)
if
(
cutadept
.
default_clip_mode
==
"3"
)
cutadept
.
opt_adapter
++=
foundAdapters
else
if
(
cutadept
.
default_clip_mode
==
"5"
)
cutadept
.
opt_front
++=
foundAdapters
else
if
(
cutadept
.
default_clip_mode
==
"both"
)
cutadept
.
opt_anywhere
++=
foundAdapters
...
...
@@ -59,27 +64,30 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
val
trim
=
if
(!
flexiprep
.
skipTrim
)
{
val
sickle
=
new
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
Sickle
(
root
)
sickle
.
output_stats
=
new
File
(
flexiprep
.
outputDir
,
s
"${flexiprep.sampleId.getOrElse("
x
")}-${flexiprep.libId.getOrElse("
x
")}.trim.stats"
)
sickle
.
output_stats
=
new
File
(
flexiprep
.
outputDir
,
s
"${flexiprep.sampleId.getOrElse("
x
")}-${flexiprep.libId.getOrElse("
x
")}.
$read.
trim.stats"
)
Some
(
sickle
)
}
else
None
val
gzip
=
new
Gzip
(
root
)
val
outputCommand
=
{
if
(
compress
)
new
Gzip
(
root
)
else
new
Cat
(
root
)
}
val
cmd
=
(
clip
,
trim
)
match
{
case
(
Some
(
clip
),
Some
(
trim
))
=>
{
clip
.
fastq_output
=
Right
(
trim
)
trim
.
output_R1
=
Right
(
gzip
>
output
)
trim
.
output_R1
=
Right
(
outputCommand
>
output
)
seqtk
|
clip
}
case
(
Some
(
clip
),
_
)
=>
{
clip
.
fastq_output
=
Right
(
gzip
>
output
)
clip
.
fastq_output
=
Right
(
outputCommand
>
output
)
seqtk
|
clip
}
case
(
_
,
Some
(
trim
))
=>
{
trim
.
output_R1
=
Right
(
gzip
>
output
)
trim
.
output_R1
=
Right
(
outputCommand
>
output
)
seqtk
|
trim
}
case
_
=>
{
seqtk
|
gzip
>
output
seqtk
|
outputCommand
>
output
}
}
...
...
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