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biopet.biopet
Commits
1a5f1520
Commit
1a5f1520
authored
Dec 04, 2015
by
Peter van 't Hof
Browse files
Add empty Qiime pipeline
parent
7e7bf6a4
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
1a5f1520
...
...
@@ -28,7 +28,6 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
* Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given.
*/
def
addMultiSampleJobs
()
:
Unit
=
{
}
/**
...
...
@@ -55,6 +54,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
lazy
val
gs
=
new
GearsSingle
(
qscript
)
gs
.
sampleId
=
Some
(
sampleId
)
gs
.
libId
=
Some
(
libId
)
gs
.
outputDir
=
libDir
gs
.
fastqR1
=
config
(
"R1"
)
gs
.
fastqR2
=
config
(
"R2"
)
gs
.
bamFile
=
config
(
"bam"
)
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRatx.scala
0 → 100644
View file @
1a5f1520
package
nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.BiopetQScript
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 12/4/15.
*/
class
GearsQiimeRatx
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
var
fastaR1
:
File
=
_
var
fastqR2
:
Option
[
File
]
=
None
def
init
()
=
{
require
(
fastaR1
!=
null
)
}
def
biopetScript
()
=
{
}
}
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
1a5f1520
...
...
@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import
nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
import
nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -44,6 +45,9 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
@Argument
(
required
=
false
)
var
outputName
:
String
=
_
var
gearsUseKraken
:
Boolean
=
config
(
"gears_use_kraken"
,
default
=
true
)
var
gearsUserQiimeRtax
:
Boolean
=
config
(
"gear_use_qiime_rtax"
,
default
=
true
)
/** Executed before running the script */
def
init
()
:
Unit
=
{
require
(
fastqR1
.
isDefined
||
bamFile
.
isDefined
,
"Please specify fastq-file(s) or bam file"
)
...
...
@@ -61,9 +65,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
if
(
fastqR1
.
isDefined
)
{
fastqR1
.
foreach
(
inputFiles
:+=
InputFile
(
_
))
fastqR2
.
foreach
(
inputFiles
:+=
InputFile
(
_
))
}
else
{
inputFiles
:+=
InputFile
(
bamFile
.
get
)
}
}
else
inputFiles
:+=
InputFile
(
bamFile
.
get
)
}
override
def
reportClass
=
{
...
...
@@ -81,7 +83,9 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
case
(
Some
(
r1
),
r2
,
_
)
=>
(
r1
,
r2
)
case
(
_
,
_
,
Some
(
bam
))
=>
val
extract
=
new
ExtractUnmappedReads
(
this
)
extract
.
outputDir
=
outputDir
extract
.
bamFile
=
bam
extract
.
outputName
=
outputName
extract
.
init
()
extract
.
biopetScript
()
addAll
(
extract
.
functions
)
...
...
@@ -89,13 +93,25 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
case
_
=>
Logging
.
addError
(
"Missing input files"
)
}
val
kraken
=
new
GearsKraken
(
this
)
kraken
.
fastqR1
=
r1
kraken
.
fastqR2
=
r2
kraken
.
init
()
kraken
.
biopetScript
()
addAll
(
kraken
.
functions
)
addSummaryQScript
(
kraken
)
lazy
val
fastqR1
=
fastqToFasta
(
r1
,
outputName
+
".R1"
)
lazy
val
fastqR2
=
r2
.
map
(
fastqToFasta
(
_
,
outputName
+
".R2"
))
if
(
gearsUseKraken
)
{
val
kraken
=
new
GearsKraken
(
this
)
kraken
.
outputDir
=
new
File
(
outputDir
,
"kraken"
)
kraken
.
fastqR1
=
r1
kraken
.
fastqR2
=
r2
kraken
.
outputName
=
outputName
kraken
.
init
()
kraken
.
biopetScript
()
addAll
(
kraken
.
functions
)
addSummaryQScript
(
kraken
)
}
if
(
gearsUserQiimeRtax
)
{
val
qiimeRatx
=
new
GearsQiimeRatx
(
this
)
}
addSummaryJobs
()
}
...
...
@@ -111,6 +127,18 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
(
if
(
bamFile
.
isDefined
)
Map
(
"input_bam"
->
bamFile
.
get
)
else
Map
())
++
(
if
(
fastqR1
.
isDefined
)
Map
(
"input_R1"
->
fastqR1
.
get
)
else
Map
())
++
outputFiles
def
fastqToFasta
(
file
:
File
,
name
:
String
)
:
File
=
{
val
seqtk
=
new
SeqtkSeq
(
this
)
{
override
def
configName
=
"seqtkseq"
override
def
fixedValues
=
Map
(
"A"
->
true
)
}
seqtk
.
input
=
file
seqtk
.
output
=
new
File
(
outputDir
,
name
+
".fasta"
)
seqtk
.
isIntermediate
=
true
add
(
seqtk
)
seqtk
.
output
}
}
/** This object give a default main method to the pipelines */
...
...
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