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biopet.biopet
Commits
3c83721a
Commit
3c83721a
authored
Sep 18, 2015
by
Peter van 't Hof
Browse files
Adding input files to check
parent
37b9a6d3
Changes
3
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Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
3c83721a
...
...
@@ -85,6 +85,9 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
paired
=
input_R2
.
isDefined
inputFiles
:+=
InputFile
(
input_R1
)
input_R2
.
foreach
(
inputFiles
:+=
InputFile
(
_
))
if
(
input_R1
.
endsWith
(
".gz"
))
R1_name
=
input_R1
.
getName
.
substring
(
0
,
input_R1
.
getName
.
lastIndexOf
(
".gz"
))
else
if
(
input_R1
.
endsWith
(
".gzip"
))
R1_name
=
input_R1
.
getName
.
substring
(
0
,
input_R1
.
getName
.
lastIndexOf
(
".gzip"
))
else
R1_name
=
input_R1
.
getName
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
3c83721a
...
...
@@ -137,6 +137,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
require
(
sampleId
.
isDefined
,
"Missing sample ID on mapping module"
)
require
(
libId
.
isDefined
,
"Missing library ID on mapping module"
)
inputFiles
:+=
InputFile
(
input_R1
)
input_R2
.
foreach
(
inputFiles
:+=
InputFile
(
_
))
paired
=
input_R2
.
isDefined
if
(
readgroupId
==
null
)
readgroupId
=
sampleId
.
get
+
"-"
+
libId
.
get
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
3c83721a
...
...
@@ -136,8 +136,12 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
case
(
true
,
_
)
=>
mapping
.
foreach
(
mapping
=>
{
mapping
.
input_R1
=
config
(
"R1"
)
mapping
.
input_R2
=
config
(
"R2"
)
inputFiles
:+=
InputFile
(
mapping
.
input_R1
,
config
(
"R1_md5"
))
mapping
.
input_R2
.
foreach
(
inputFiles
:+=
InputFile
(
_
,
config
(
"R2_md5"
)))
})
case
(
false
,
true
)
=>
config
(
"bam_to_fastq"
,
default
=
false
).
asBoolean
match
{
case
(
false
,
true
)
=>
{
inputFiles
:+=
InputFile
(
config
(
"bam"
),
config
(
"bam_md5"
))
config
(
"bam_to_fastq"
,
default
=
false
).
asBoolean
match
{
case
true
=>
val
samToFastq
=
SamToFastq
(
qscript
,
config
(
"bam"
),
new
File
(
libDir
,
sampleId
+
"-"
+
libId
+
".R1.fastq"
),
...
...
@@ -182,6 +186,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
add
(
bamLn
)
}
}
}
case
_
=>
logger
.
warn
(
"Sample: "
+
sampleId
+
" Library: "
+
libId
+
", no reads found"
)
}
...
...
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