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biopet.biopet
Commits
4f99194a
Commit
4f99194a
authored
Mar 09, 2017
by
Peter van 't Hof
Browse files
Fixing clipping module in summary
parent
be748324
Changes
1
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
4f99194a
...
...
@@ -16,12 +16,12 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryQScript
,
Summarizable
}
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
BiopetCommandLineFunction
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Gzip
,
Sickle
}
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
BiopetFifoPipe
,
BiopetQScript
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Gzip
,
Sickle
}
import
nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Out
put
,
In
put
}
import
org.broadinstitute.gatk.utils.commandline.
{
In
put
,
Out
put
}
/**
* Created by pjvan_thof on 9/22/15.
...
...
@@ -106,24 +106,25 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
if
(
seqtk
.
Q
.
isDefined
)
seqtk
.
V
=
true
addPipeJob
(
seqtk
)
clip
=
if
(!
flexiprep
.
skipClip
)
{
val
cutadapt
=
clip
.
getOrElse
(
new
Cutadapt
(
parent
,
fastqc
))
val
foundAdapters
:
Set
[
String
]
=
if
(!
cutadapt
.
ignoreFastqcAdapters
)
{
fastqc
.
foundAdapters
.
map
(
_
.
seq
)
}
else
Set
()
if
(
foundAdapters
.
nonEmpty
||
cutadapt
.
adapter
.
nonEmpty
||
cutadapt
.
front
.
nonEmpty
||
cutadapt
.
anywhere
.
nonEmpty
)
{
cutadapt
.
fastqInput
=
seqtk
.
output
cutadapt
.
fastqOutput
=
new
File
(
output
.
getParentFile
,
input
.
getName
+
".cutadapt.fq"
)
cutadapt
.
statsOutput
=
new
File
(
flexiprep
.
outputDir
,
s
"${flexiprep.sampleId.getOrElse("
x
")}-${flexiprep.libId.getOrElse("
x
")}.$read.clip.stats"
)
if
(
cutadapt
.
defaultClipMode
==
"3"
)
cutadapt
.
adapter
++=
foundAdapters
else
if
(
cutadapt
.
defaultClipMode
==
"5"
)
cutadapt
.
front
++=
foundAdapters
else
if
(
cutadapt
.
defaultClipMode
==
"both"
)
cutadapt
.
anywhere
++=
foundAdapters
addPipeJob
(
cutadapt
)
Some
(
cutadapt
)
}
else
None
}
else
None
clip
=
(
clip
,
BiopetQScript
.
safeIsDone
(
fastqc
))
match
{
case
(
Some
(
cutadapt
),
Some
(
true
))
=>
val
foundAdapters
:
Set
[
String
]
=
if
(!
cutadapt
.
ignoreFastqcAdapters
)
{
fastqc
.
foundAdapters
.
map
(
_
.
seq
)
}
else
Set
()
if
(
foundAdapters
.
nonEmpty
||
cutadapt
.
adapter
.
nonEmpty
||
cutadapt
.
front
.
nonEmpty
||
cutadapt
.
anywhere
.
nonEmpty
)
{
cutadapt
.
fastqInput
=
seqtk
.
output
cutadapt
.
fastqOutput
=
new
File
(
output
.
getParentFile
,
input
.
getName
+
".cutadapt.fq"
)
cutadapt
.
statsOutput
=
new
File
(
flexiprep
.
outputDir
,
s
"${flexiprep.sampleId.getOrElse("
x
")}-${flexiprep.libId.getOrElse("
x
")}.$read.clip.stats"
)
if
(
cutadapt
.
defaultClipMode
==
"3"
)
cutadapt
.
adapter
++=
foundAdapters
else
if
(
cutadapt
.
defaultClipMode
==
"5"
)
cutadapt
.
front
++=
foundAdapters
else
if
(
cutadapt
.
defaultClipMode
==
"both"
)
cutadapt
.
anywhere
++=
foundAdapters
addPipeJob
(
cutadapt
)
Some
(
cutadapt
)
}
else
None
case
(
None
,
_
)
=>
None
case
(
c
,
_
)
=>
c
}
trim
.
foreach
{
t
=>
t
.
outputR1
=
new
File
(
output
.
getParentFile
,
input
.
getName
+
".sickle.fq"
)
...
...
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