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biopet.biopet
Commits
5448ee58
Commit
5448ee58
authored
Oct 27, 2015
by
Peter van 't Hof
Browse files
Added input files to summary of shiva
parent
ba50ff98
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
5448ee58
...
...
@@ -91,11 +91,13 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
/** Library specific files to add to the summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
{
(
bamFile
,
preProcessBam
)
match
{
(
(
bamFile
,
preProcessBam
)
match
{
case
(
Some
(
b
),
Some
(
pb
))
=>
Map
(
"bamFile"
->
b
,
"preProcessBam"
->
pb
)
case
(
Some
(
b
),
_
)
=>
Map
(
"bamFile"
->
b
)
case
_
=>
Map
()
}
})
++
(
inputR1
.
map
(
"input_R1"
->
_
)
::
inputR2
.
map
(
"input_R2"
->
_
)
::
inputBam
.
map
(
"input_bam"
->
_
)
::
Nil
).
flatten
.
toMap
}
/** Library specific stats to add to summary */
...
...
@@ -117,8 +119,12 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
(
Some
(
mapping
),
Some
(
mapping
.
finalBamFile
),
preProcess
(
mapping
.
finalBamFile
))
}
lazy
val
inputR1
:
Option
[
File
]
=
config
(
"R1"
)
lazy
val
inputR2
:
Option
[
File
]
=
config
(
"R2"
)
lazy
val
inputBam
:
Option
[
File
]
=
if
(
r1
.
isEmpty
)
config
(
"bam"
)
else
None
lazy
val
(
mapping
,
bamFile
,
preProcessBam
)
:
(
Option
[
Mapping
],
Option
[
File
],
Option
[
File
])
=
(
config
.
contains
(
"R1"
),
config
.
contains
(
"bam"
)
)
match
{
(
inputR1
.
isDefined
,
inputBam
.
isDefined
)
match
{
case
(
true
,
_
)
=>
makeMapping
// Default starting from fastq files
case
(
false
,
true
)
=>
// Starting from bam file
config
(
"bam_to_fastq"
,
default
=
false
).
asBoolean
match
{
...
...
@@ -137,18 +143,18 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
/** This will add jobs for this library */
def
addJobs
()
:
Unit
=
{
(
config
.
contains
(
"R1"
),
config
.
contains
(
"bam"
)
)
match
{
(
inputR1
.
isDefined
,
inputBam
.
isDefined
)
match
{
case
(
true
,
_
)
=>
mapping
.
foreach
(
mapping
=>
{
mapping
.
input_R1
=
config
(
"R1"
)
mapping
.
input_R2
=
config
(
"R2"
)
mapping
.
input_R1
=
inputR1
.
get
mapping
.
input_R2
=
inputR2
inputFiles
:+=
new
InputFile
(
mapping
.
input_R1
,
config
(
"R1_md5"
))
mapping
.
input_R2
.
foreach
(
inputFiles
:+=
new
InputFile
(
_
,
config
(
"R2_md5"
)))
})
case
(
false
,
true
)
=>
{
inputFiles
:+=
new
InputFile
(
config
(
"bam"
)
,
config
(
"bam_md5"
))
inputFiles
:+=
new
InputFile
(
inputBam
.
get
,
config
(
"bam_md5"
))
config
(
"bam_to_fastq"
,
default
=
false
).
asBoolean
match
{
case
true
=>
val
samToFastq
=
SamToFastq
(
qscript
,
config
(
"bam"
)
,
val
samToFastq
=
SamToFastq
(
qscript
,
inputBam
.
get
,
new
File
(
libDir
,
sampleId
+
"-"
+
libId
+
".R1.fq.gz"
),
new
File
(
libDir
,
sampleId
+
"-"
+
libId
+
".R2.fq.gz"
))
samToFastq
.
isIntermediate
=
true
...
...
@@ -158,7 +164,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
mapping
.
input_R2
=
Some
(
samToFastq
.
fastqR2
)
})
case
false
=>
val
inputSam
=
SamReaderFactory
.
makeDefault
.
open
(
config
(
"bam"
)
)
val
inputSam
=
SamReaderFactory
.
makeDefault
.
open
(
inputBam
.
get
)
val
readGroups
=
inputSam
.
getFileHeader
.
getReadGroups
val
readGroupOke
=
readGroups
.
forall
(
readGroup
=>
{
...
...
@@ -170,8 +176,8 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
if
(!
readGroupOke
)
{
if
(
config
(
"correct_readgroups"
,
default
=
false
).
asBoolean
)
{
logger
.
info
(
"Correcting readgroups, file:"
+
config
(
"bam"
)
)
val
aorrg
=
AddOrReplaceReadGroups
(
qscript
,
config
(
"bam"
)
,
bamFile
.
get
)
logger
.
info
(
"Correcting readgroups, file:"
+
inputBam
.
get
)
val
aorrg
=
AddOrReplaceReadGroups
(
qscript
,
inputBam
.
get
,
bamFile
.
get
)
aorrg
.
RGID
=
sampleId
+
"-"
+
libId
aorrg
.
RGLB
=
libId
aorrg
.
RGSM
=
sampleId
...
...
@@ -180,7 +186,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
}
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
oldBamFile
:
File
=
inputBam
.
get
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
)
...
...
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