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biopet.biopet
Commits
063083df
Commit
063083df
authored
Apr 18, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 18, 2017
Browse files
Merge branch 'develop' into fix-BIOPET-306
parents
2e681cb4
4fb8a7b6
Changes
4
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Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
063083df
...
...
@@ -126,17 +126,21 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
})
logger
.
info
(
"Adding report"
)
this
match
{
case
q
:
MultiSampleQScript
if
q.onlySamples.nonEmpty
&&
!q.samples.forall
(
x
=>
q.onlySamples.contains
(
x.
_
1
))
=>
logger
.
info
(
"Write report is skipped because sample flag is used"
)
case
_
=>
reportClass
.
foreach
{
report
=>
for
(
f
<-
functions
)
f
match
{
case
w
:
WriteSummary
=>
report
.
deps
:+=
w
.
jobOutputFile
case
_
=>
val
writeHtmlReport
:
Boolean
=
config
(
"write_html_report"
,
default
=
true
)
if
(
writeHtmlReport
)
{
logger
.
info
(
"Adding report"
)
this
match
{
case
q
:
MultiSampleQScript
if
q.onlySamples.nonEmpty
&&
!q.samples.forall
(
x
=>
q.onlySamples.contains
(
x.
_
1
))
=>
logger
.
info
(
"Write report is skipped because sample flag is used"
)
case
_
=>
reportClass
.
foreach
{
report
=>
for
(
f
<-
functions
)
f
match
{
case
w
:
WriteSummary
=>
report
.
deps
:+=
w
.
jobOutputFile
case
_
=>
}
report
.
jobOutputFile
=
new
File
(
report
.
outputDir
,
".report.out"
)
add
(
report
)
}
report
.
jobOutputFile
=
new
File
(
report
.
outputDir
,
".report.out"
)
add
(
report
)
}
}
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @
063083df
...
...
@@ -33,7 +33,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var
R2
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
shortName
=
"R"
)
var
reference
:
File
=
null
var
reference
:
File
=
_
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
)
var
output
:
File
=
_
...
...
@@ -42,7 +42,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var
k
:
Option
[
Int
]
=
config
(
"k"
)
var
r
:
Option
[
Float
]
=
config
(
"r"
)
var
S
:
Boolean
=
config
(
"S"
,
default
=
false
)
var
M
:
Boolean
=
config
(
"M"
,
default
=
tru
e
)
var
M
:
Boolean
=
config
(
"M"
,
default
=
fals
e
)
var
w
:
Option
[
Int
]
=
config
(
"w"
)
var
d
:
Option
[
Int
]
=
config
(
"d"
)
var
c
:
Option
[
Int
]
=
config
(
"c"
)
...
...
@@ -75,7 +75,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
def
cmdLine
=
{
def
cmdLine
:
String
=
{
required
(
executable
)
+
required
(
"mem"
)
+
optional
(
"-k"
,
k
)
+
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
063083df
...
...
@@ -56,12 +56,7 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
if
(
sampleId
==
null
||
sampleId
==
None
)
Logging
.
addError
(
"Missing sample ID on GearsSingle module"
)
if
(
outputName
==
null
)
{
if
(
fastqR1
.
nonEmpty
)
outputName
=
fastqR1
.
headOption
.
map
(
_
.
getName
.
stripSuffix
(
".gz"
)
.
stripSuffix
(
".fastq"
)
.
stripSuffix
(
".fq"
))
.
getOrElse
(
"noName"
)
else
outputName
=
bamFile
.
map
(
_
.
getName
.
stripSuffix
(
".bam"
)).
getOrElse
(
"noName"
)
outputName
=
sampleId
.
getOrElse
(
"noName"
)
+
libId
.
map
(
"-"
+
_
).
getOrElse
(
""
)
}
if
(
fastqR1
.
nonEmpty
)
{
...
...
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
View file @
063083df
...
...
@@ -108,7 +108,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
gears
.
outputName
shouldBe
"test"
}
else
{
// in the following cases the filename should have been determined by the filename
gears
.
outputName
shouldBe
(
if
(
inputMode
==
Some
(
"bam"
))
"bamfile"
else
"R1"
)
gears
.
outputName
shouldBe
"sampleName-libName"
}
val
pipesJobs
=
gears
.
functions
.
filter
(
_
.
isInstanceOf
[
BiopetCommandLineFunction
])
...
...
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