Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
5d5c30c1
Commit
5d5c30c1
authored
Oct 02, 2015
by
Peter van 't Hof
Browse files
Fixed summary files of flexiprep
parent
a7da2f6a
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
5d5c30c1
...
...
@@ -47,11 +47,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Returns files to store in summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
{
if
(!
skipTrim
||
!
skipClip
)
Map
(
"input_R1"
->
input_R1
,
"output_R1"
->
outputFiles
(
"output_R1_gzip"
))
++
(
if
(
paired
)
Map
(
"input_R2"
->
input_R2
.
get
,
"output_R2"
->
outputFiles
(
"output_R2_gzip"
))
else
Map
())
else
Map
(
"input_R1"
->
input_R1
)
++
(
if
(
paired
)
Map
(
"input_R2"
->
input_R2
.
get
)
else
Map
())
Map
(
"input_R1"
->
input_R1
,
"output_R1"
->
fastqR1Qc
)
++
(
if
(
paired
)
Map
(
"input_R2"
->
input_R2
.
get
,
"output_R2"
->
fastqR2Qc
.
get
)
else
Map
())
}
/** returns settings to store in summary */
...
...
@@ -112,8 +109,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def
biopetScript
()
{
runInitialJobs
()
val
out
=
if
(
paired
)
runTrimClip
(
outputFiles
(
"fastq_input_R1"
),
Some
(
outputFiles
(
"fastq_
input_R2
"
))
,
outputDir
)
else
runTrimClip
(
outputFiles
(
"fastq_
input_R1
"
)
,
outputDir
)
val
out
=
if
(
paired
)
runTrimClip
(
input_R1
,
input_R2
,
outputDir
)
else
runTrimClip
(
input_R1
,
outputDir
)
val
R1_files
=
for
((
k
,
v
)
<-
outputFiles
if
k
.
endsWith
(
"output_R1"
))
yield
v
val
R2_files
=
for
((
k
,
v
)
<-
outputFiles
if
k
.
endsWith
(
"output_R2"
))
yield
v
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
5d5c30c1
...
...
@@ -196,7 +196,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
extractIfNeeded
(
input_R1
,
flexiprep
.
outputDir
),
if
(
paired
)
Some
(
extractIfNeeded
(
input_R2
.
get
,
outputDir
))
else
None
)
)
}
else
Map
(
outputDir
->
(
flexiprep
.
outputFiles
(
"fastq_input_R1"
),
flexiprep
.
outputFiles
.
get
(
"fastq_input_R2"
)
))
}
else
Map
(
outputDir
->
(
flexiprep
.
fastqR1Qc
,
flexiprep
.
fastqR2Qc
))
}
if
(
chunking
)
{
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment