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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
Hide whitespace changes
Inline
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
...
...
@@ -136,51 +136,56 @@ 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
true
=>
val
samToFastq
=
SamToFastq
(
qscript
,
config
(
"bam"
),
new
File
(
libDir
,
sampleId
+
"-"
+
libId
+
".R1.fastq"
),
new
File
(
libDir
,
sampleId
+
"-"
+
libId
+
".R2.fastq"
))
samToFastq
.
isIntermediate
=
true
qscript
.
add
(
samToFastq
)
mapping
.
foreach
(
mapping
=>
{
mapping
.
input_R1
=
samToFastq
.
fastqR1
mapping
.
input_R2
=
Some
(
samToFastq
.
fastqR2
)
})
case
false
=>
val
inputSam
=
SamReaderFactory
.
makeDefault
.
open
(
config
(
"bam"
))
val
readGroups
=
inputSam
.
getFileHeader
.
getReadGroups
val
readGroupOke
=
readGroups
.
forall
(
readGroup
=>
{
if
(
readGroup
.
getSample
!=
sampleId
)
logger
.
warn
(
"Sample ID readgroup in bam file is not the same"
)
if
(
readGroup
.
getLibrary
!=
libId
)
logger
.
warn
(
"Library ID readgroup in bam file is not the same"
)
readGroup
.
getSample
==
sampleId
&&
readGroup
.
getLibrary
==
libId
})
inputSam
.
close
()
if
(!
readGroupOke
)
{
if
(
config
(
"correct_readgroups"
,
default
=
false
).
asBoolean
)
{
logger
.
info
(
"Correcting readgroups, file:"
+
config
(
"bam"
))
val
aorrg
=
AddOrReplaceReadGroups
(
qscript
,
config
(
"bam"
),
bamFile
.
get
)
aorrg
.
RGID
=
sampleId
+
"-"
+
libId
aorrg
.
RGLB
=
libId
aorrg
.
RGSM
=
sampleId
aorrg
.
isIntermediate
=
true
qscript
.
add
(
aorrg
)
}
else
throw
new
IllegalStateException
(
"Sample readgroup and/or library of input bamfile is not correct, file: "
+
bamFile
+
"\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this"
)
}
else
{
val
oldBamFile
:
File
=
config
(
"bam"
)
val
oldIndex
:
File
=
new
File
(
oldBamFile
.
getAbsolutePath
.
stripSuffix
(
".bam"
)
+
".bai"
)
val
newIndex
:
File
=
new
File
(
libDir
,
oldBamFile
.
getName
.
stripSuffix
(
".bam"
)
+
".bai"
)
val
baiLn
=
Ln
(
qscript
,
oldIndex
,
newIndex
)
add
(
baiLn
)
val
bamLn
=
Ln
(
qscript
,
oldBamFile
,
bamFile
.
get
)
bamLn
.
deps
:+=
baiLn
.
output
add
(
bamLn
)
}
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"
),
new
File
(
libDir
,
sampleId
+
"-"
+
libId
+
".R2.fastq"
))
samToFastq
.
isIntermediate
=
true
qscript
.
add
(
samToFastq
)
mapping
.
foreach
(
mapping
=>
{
mapping
.
input_R1
=
samToFastq
.
fastqR1
mapping
.
input_R2
=
Some
(
samToFastq
.
fastqR2
)
})
case
false
=>
val
inputSam
=
SamReaderFactory
.
makeDefault
.
open
(
config
(
"bam"
))
val
readGroups
=
inputSam
.
getFileHeader
.
getReadGroups
val
readGroupOke
=
readGroups
.
forall
(
readGroup
=>
{
if
(
readGroup
.
getSample
!=
sampleId
)
logger
.
warn
(
"Sample ID readgroup in bam file is not the same"
)
if
(
readGroup
.
getLibrary
!=
libId
)
logger
.
warn
(
"Library ID readgroup in bam file is not the same"
)
readGroup
.
getSample
==
sampleId
&&
readGroup
.
getLibrary
==
libId
})
inputSam
.
close
()
if
(!
readGroupOke
)
{
if
(
config
(
"correct_readgroups"
,
default
=
false
).
asBoolean
)
{
logger
.
info
(
"Correcting readgroups, file:"
+
config
(
"bam"
))
val
aorrg
=
AddOrReplaceReadGroups
(
qscript
,
config
(
"bam"
),
bamFile
.
get
)
aorrg
.
RGID
=
sampleId
+
"-"
+
libId
aorrg
.
RGLB
=
libId
aorrg
.
RGSM
=
sampleId
aorrg
.
isIntermediate
=
true
qscript
.
add
(
aorrg
)
}
else
throw
new
IllegalStateException
(
"Sample readgroup and/or library of input bamfile is not correct, file: "
+
bamFile
+
"\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this"
)
}
else
{
val
oldBamFile
:
File
=
config
(
"bam"
)
val
oldIndex
:
File
=
new
File
(
oldBamFile
.
getAbsolutePath
.
stripSuffix
(
".bam"
)
+
".bai"
)
val
newIndex
:
File
=
new
File
(
libDir
,
oldBamFile
.
getName
.
stripSuffix
(
".bam"
)
+
".bai"
)
val
baiLn
=
Ln
(
qscript
,
oldIndex
,
newIndex
)
add
(
baiLn
)
val
bamLn
=
Ln
(
qscript
,
oldBamFile
,
bamFile
.
get
)
bamLn
.
deps
:+=
baiLn
.
output
add
(
bamLn
)
}
}
}
case
_
=>
logger
.
warn
(
"Sample: "
+
sampleId
+
" Library: "
+
libId
+
", no reads found"
)
}
...
...
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