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biopet.biopet
Commits
b3ae6caf
Commit
b3ae6caf
authored
Jan 19, 2015
by
Peter van 't Hof
Browse files
Remove unused vars
parent
8e8b825e
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
b3ae6caf
...
...
@@ -132,7 +132,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
var
results
:
Map
[
String
,
File
]
=
Map
()
var
R1
:
File
=
new
File
(
R1_in
)
var
R2
:
File
=
new
File
(
R2_in
)
var
R2
:
File
=
if
(
paired
)
new
File
(
R2_in
)
else
null
var
deps
:
List
[
File
]
=
if
(
paired
)
List
(
R1
,
R2
)
else
List
(
R1
)
val
seqtkSeq_R1
=
SeqtkSeq
(
this
,
R1
,
swapExt
(
outDir
,
R1
,
R1_ext
,
".sanger"
+
R1_ext
),
fastqc_R1
)
...
...
@@ -199,7 +199,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
}
sickle
.
output_stats
=
swapExt
(
outDir
,
R1
,
R1_ext
,
".trim.stats"
)
sickle
.
deps
=
deps
add
(
sickle
,
isIntermediate
=
true
)
sickle
.
isIntermediate
=
true
add
(
sickle
)
summary
.
addSickle
(
sickle
,
chunk
)
R1
=
sickle
.
output_R1
if
(
paired
)
R2
=
sickle
.
output_R2
...
...
@@ -256,7 +257,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
}
def
extractIfNeeded
(
file
:
File
,
runDir
:
String
)
:
File
=
{
if
(
file
.
getName
().
endsWith
(
".gz"
)
||
file
.
getName
().
endsWith
(
".gzip"
))
{
if
(
file
==
null
)
return
file
else
if
(
file
.
getName
().
endsWith
(
".gz"
)
||
file
.
getName
().
endsWith
(
".gzip"
))
{
var
newFile
:
File
=
swapExt
(
runDir
,
file
,
".gz"
,
""
)
if
(
file
.
getName
().
endsWith
(
".gzip"
))
newFile
=
swapExt
(
runDir
,
file
,
".gzip"
,
""
)
val
zcatCommand
=
Zcat
(
this
,
file
,
newFile
)
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
b3ae6caf
...
...
@@ -122,12 +122,10 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
}
def
biopetScript
()
{
var
fastq_R1
:
File
=
input_R1
var
fastq_R2
:
File
=
if
(
paired
)
input_R2
else
""
if
(!
skipFlexiprep
)
{
flexiprep
.
outputDir
=
outputDir
+
"flexiprep/"
flexiprep
.
input_R1
=
fastq
_R1
if
(
paired
)
flexiprep
.
input_R2
=
fastq
_R2
flexiprep
.
input_R1
=
input
_R1
if
(
paired
)
flexiprep
.
input_R2
=
input
_R2
flexiprep
.
sampleName
=
this
.
RGSM
flexiprep
.
libraryName
=
this
.
RGLB
flexiprep
.
init
...
...
@@ -145,22 +143,22 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var
chunks
:
Map
[
String
,
(
String
,
String
)]
=
Map
()
if
(
chunking
)
for
(
t
<-
1
to
numberChunks
.
getOrElse
(
1
))
{
val
chunkDir
=
outputDir
+
"chunks/"
+
t
+
"/"
chunks
+=
(
chunkDir
->
(
removeGz
(
chunkDir
+
fastq
_R1
.
getName
),
if
(
paired
)
removeGz
(
chunkDir
+
fastq
_R2
.
getName
)
else
""
))
chunks
+=
(
chunkDir
->
(
removeGz
(
chunkDir
+
input
_R1
.
getName
),
if
(
paired
)
removeGz
(
chunkDir
+
input
_R2
.
getName
)
else
""
))
}
else
chunks
+=
(
outputDir
->
(
flexiprep
.
extractIfNeeded
(
fastq
_R1
,
flexiprep
.
outputDir
),
flexiprep
.
extractIfNeeded
(
fastq
_R2
,
flexiprep
.
outputDir
)))
else
chunks
+=
(
outputDir
->
(
flexiprep
.
extractIfNeeded
(
input
_R1
,
flexiprep
.
outputDir
),
flexiprep
.
extractIfNeeded
(
input
_R2
,
flexiprep
.
outputDir
)))
if
(
chunking
)
{
val
fastSplitter_R1
=
new
FastqSplitter
(
this
)
fastSplitter_R1
.
input
=
fastq
_R1
fastSplitter_R1
.
input
=
input
_R1
for
((
chunkDir
,
fastqfile
)
<-
chunks
)
fastSplitter_R1
.
output
:+=
fastqfile
.
_1
fastSplitter_R1
.
isIntermediate
=
true
add
(
fastSplitter_R1
)
if
(
paired
)
{
val
fastSplitter_R2
=
new
FastqSplitter
(
this
)
fastSplitter_R2
.
input
=
fastq
_R2
fastSplitter_R2
.
input
=
input
_R2
for
((
chunkDir
,
fastqfile
)
<-
chunks
)
fastSplitter_R2
.
output
:+=
fastqfile
.
_2
fastSplitter_R2
.
isIntermediate
=
true
add
(
fastSplitter_R2
)
...
...
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