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
d1c0ec8b
Commit
d1c0ec8b
authored
Feb 17, 2015
by
Peter van 't Hof
Browse files
Added output Files
parent
8145ca77
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
d1c0ec8b
...
...
@@ -43,7 +43,10 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"x"
)
+
"-"
+
libId
.
getOrElse
(
"x"
)
+
".qc.summary.json"
)
def
summaryFiles
=
Map
()
def
summaryFiles
:
Map
[
String
,
File
]
=
{
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
())
}
def
summaryData
=
Map
(
"skip_trim"
->
skipTrim
,
"skip_clip"
->
skipClip
,
"paired"
->
paired
)
...
...
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