Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
What's new
7
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Open sidebar
Mirrors
biopet.biopet
Commits
21fa48ed
Commit
21fa48ed
authored
Dec 05, 2016
by
Sander Bollen
Browse files
Options
Browse Files
Download
Plain Diff
Merge branch 'fix-BIOPET-412' into 'develop'
Fix BIOPET-412 Fix BIOPET-412 See merge request !487
parents
2221fa53
b747862a
Changes
4
Hide whitespace changes
Inline
Side-by-side
Showing
4 changed files
with
7 additions
and
2 deletions
+7
-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+1
-1
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
...la/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
+4
-1
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
...l/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
+1
-0
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
.../nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
+1
-0
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
21fa48ed
...
...
@@ -57,7 +57,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
for
(
q
<-
qscript
.
summaryQScripts
)
deps
:+=
q
.
summaryFile
for
((
_
,
l
)
<-
qscript
.
summarizables
;
s
<-
l
)
s
match
{
case
f
:
QFunction
=>
try
{
case
f
:
QFunction
if
qscript.functions.contains
(
f
)
=>
try
{
deps
:+=
f
.
firstOutput
}
catch
{
case
e
:
NullPointerException
=>
logger
.
warn
(
"Queue values are not init"
)
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
View file @
21fa48ed
...
...
@@ -54,12 +54,14 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
swapExt
(
outputDir
,
flash
.
notCombinedR2
,
".fastq.gz"
,
".clip.fastq.gz"
)
else
flash
.
notCombinedR2
val
keepFastaqFiles
:
Boolean
=
config
(
"keep_fastq_files"
,
default
=
false
)
/** Pipeline itself */
def
biopetScript
()
:
Unit
=
{
flash
.
outputDirectory
=
new
File
(
outputDir
,
"flash"
)
flash
.
fastqR1
=
fastqR1
flash
.
fastqR2
=
fastqR2
flash
.
isIntermediate
=
(
forwardPrimers
:::
reversePrimers
).
nonEmpty
flash
.
isIntermediate
=
!
keepFastaqFiles
||
(
forwardPrimers
:::
reversePrimers
).
nonEmpty
add
(
flash
)
if
((
forwardPrimers
:::
reversePrimers
).
nonEmpty
)
{
...
...
@@ -67,6 +69,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
cutadapt
.
fastqInput
=
flash
.
combinedFastq
cutadapt
.
fastqOutput
=
this
.
combinedFastq
cutadapt
.
statsOutput
=
swapExt
(
outputDir
,
cutadapt
.
fastqOutput
,
".fastq.gz"
,
".stats"
)
cutadapt
.
isIntermediate
=
!
keepFastaqFiles
(
forwardPrimers
:::
reversePrimers
).
foreach
(
cutadapt
.
anywhere
+=
_
)
add
(
cutadapt
)
addSummarizable
(
cutadapt
,
"cutadapt"
)
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
View file @
21fa48ed
...
...
@@ -58,6 +58,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
splitLib
.
input
:+=
fastqInput
splitLib
.
outputDir
=
new
File
(
outputDir
,
"split_libraries_fastq"
)
sampleId
.
foreach
(
splitLib
.
sampleIds
:+=
_
.
replaceAll
(
"_"
,
"-"
))
splitLib
.
isIntermediate
=
true
add
(
splitLib
)
val
closedReference
=
new
PickClosedReferenceOtus
(
this
)
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
View file @
21fa48ed
...
...
@@ -51,6 +51,7 @@ class GearsQiimeOpen(val root: Configurable) extends QScript with SummaryQScript
splitLib
.
input
:+=
fastqInput
splitLib
.
outputDir
=
new
File
(
outputDir
,
"split_libraries_fastq"
)
sampleId
.
foreach
(
splitLib
.
sampleIds
:+=
_
.
replaceAll
(
"_"
,
"-"
))
splitLib
.
isIntermediate
=
true
add
(
splitLib
)
val
openReference
=
new
PickOpenReferenceOtus
(
this
)
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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