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biopet.biopet
Commits
4e925feb
Commit
4e925feb
authored
Jul 15, 2014
by
Peter van 't Hof
Browse files
Fixed file location when not chunking
parent
9be7a784
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
4e925feb
...
...
@@ -137,7 +137,8 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
if
(
chunking
)
for
(
t
<-
1
to
numberChunks
)
{
chunks
+=
(
"chunk_"
+
t
->
(
removeGz
(
outputDir
+
"chunk_"
+
t
+
"/"
+
fastq_R1
.
getName
),
if
(
paired
)
removeGz
(
outputDir
+
"chunk_"
+
t
+
"/"
+
fastq_R2
.
getName
)
else
""
))
}
else
chunks
+=
(
flexiprep
.
outputDir
->
(
fastq_R1
,
fastq_R2
))
}
else
chunks
+=
(
"flexiprep"
->
(
flexiprep
.
extractIfNeeded
(
fastq_R1
,
flexiprep
.
outputDir
),
flexiprep
.
extractIfNeeded
(
fastq_R2
,
flexiprep
.
outputDir
)))
if
(
chunking
)
{
val
fastSplitter_R1
=
new
FastqSplitter
(
this
)
...
...
@@ -163,6 +164,7 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
if
(!
skipFlexiprep
)
{
flexiprep
.
input_R1
=
fastq_R1
if
(
paired
)
flexiprep
.
input_R2
=
fastq_R2
flexiprep
.
skipSummary
=
true
flexiprep
.
init
flexiprep
.
runInitialJobs
//flexiprep.biopetScript
...
...
@@ -173,7 +175,7 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
fastq_R1_output
:+=
R1
fastq_R2_output
:+=
R2
}
val
chunkDir
=
if
(
chunk
.
isEmpty
)
outputDir
else
outputDir
+
chunk
+
"/"
val
chunkDir
=
if
(
chunk
ing
)
outputDir
+
chunk
+
"/"
else
outputDir
if
(
aligner
==
"bwa"
)
{
val
bwaCommand
=
new
Bwa
(
this
)
bwaCommand
.
R1
=
R1
...
...
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