Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
d4564525
Commit
d4564525
authored
Feb 17, 2015
by
Peter van 't Hof
Browse files
Move sickle summary methods to general sickle extension
parent
78fe69d8
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
View file @
d4564525
...
...
@@ -19,9 +19,13 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
Sickle
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
import
scala.collection.mutable
import
scala.io.Source
class
Sickle
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Summarizable
{
@Input
(
doc
=
"R1 input"
)
var
input_R1
:
File
=
_
...
...
@@ -76,4 +80,40 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
optional
(
"--quiet"
,
quiet
)
+
" > "
+
required
(
output_stats
)
}
def
summaryData
:
Map
[
String
,
Any
]
=
{
val
pairKept
=
"""FastQ paired records kept: (\d*) \((\d*) pairs\)"""
.
r
val
singleKept
=
"""FastQ single records kept: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)"""
.
r
val
pairDiscarded
=
"""FastQ paired records discarded: (\d*) \((\d*) pairs\)"""
.
r
val
singleDiscarded
=
"""FastQ single records discarded: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)"""
.
r
var
stats
:
mutable.Map
[
String
,
Int
]
=
mutable
.
Map
()
if
(
output_stats
.
exists
)
for
(
line
<-
Source
.
fromFile
(
output_stats
).
getLines
)
{
line
match
{
case
pairKept
(
reads
,
pairs
)
=>
stats
+=
(
"num_paired_reads_kept"
->
reads
.
toInt
)
case
singleKept
(
total
,
r1
,
r2
)
=>
{
stats
+=
(
"num_reads_kept_R1"
->
r1
.
toInt
)
stats
+=
(
"num_reads_kept_R2"
->
r2
.
toInt
)
}
case
pairDiscarded
(
reads
,
pairs
)
=>
stats
+=
(
"num_paired_reads_discarded"
->
reads
.
toInt
)
case
singleDiscarded
(
total
,
r1
,
r2
)
=>
{
stats
+=
(
"num_reads_discarded_R1"
->
r1
.
toInt
)
stats
+=
(
"num_reads_discarded_R2"
->
r2
.
toInt
)
}
case
_
=>
}
}
stats
.
toMap
++
Map
(
"version"
->
getVersion
)
}
override
def
resolveSummaryConflict
(
v1
:
Any
,
v2
:
Any
,
key
:
String
)
:
Any
=
{
(
v1
,
v2
)
match
{
case
(
v1
:
Int
,
v2
:
Int
)
=>
v1
+
v2
case
_
=>
v1
}
}
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
}
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
d4564525
...
...
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
import
nl.lumc.sasc.biopet.core.
{
SampleLibraryTag
,
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.
{
Gzip
,
Pbzip2
,
Md5sum
,
Zcat
,
Seqstat
}
import
nl.lumc.sasc.biopet.extensions.
_
import
nl.lumc.sasc.biopet.tools.FastqSync
class
Flexiprep
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
{
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala
deleted
100644 → 0
View file @
78fe69d8
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
argonaut._
,
Argonaut
.
_
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
scalaz._
,
Scalaz
.
_
import
scala.io.Source
import
scala.collection.mutable
class
Sickle
(
root
:
Configurable
)
extends
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
Sickle
(
root
)
with
Summarizable
{
def
summaryData
:
Map
[
String
,
Any
]
=
{
val
pairKept
=
"""FastQ paired records kept: (\d*) \((\d*) pairs\)"""
.
r
val
singleKept
=
"""FastQ single records kept: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)"""
.
r
val
pairDiscarded
=
"""FastQ paired records discarded: (\d*) \((\d*) pairs\)"""
.
r
val
singleDiscarded
=
"""FastQ single records discarded: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)"""
.
r
var
stats
:
mutable.Map
[
String
,
Int
]
=
mutable
.
Map
()
if
(
output_stats
.
exists
)
for
(
line
<-
Source
.
fromFile
(
output_stats
).
getLines
)
{
line
match
{
case
pairKept
(
reads
,
pairs
)
=>
stats
+=
(
"num_paired_reads_kept"
->
reads
.
toInt
)
case
singleKept
(
total
,
r1
,
r2
)
=>
{
stats
+=
(
"num_reads_kept_R1"
->
r1
.
toInt
)
stats
+=
(
"num_reads_kept_R2"
->
r2
.
toInt
)
}
case
pairDiscarded
(
reads
,
pairs
)
=>
stats
+=
(
"num_paired_reads_discarded"
->
reads
.
toInt
)
case
singleDiscarded
(
total
,
r1
,
r2
)
=>
{
stats
+=
(
"num_reads_discarded_R1"
->
r1
.
toInt
)
stats
+=
(
"num_reads_discarded_R2"
->
r2
.
toInt
)
}
case
_
=>
}
}
stats
.
toMap
++
Map
(
"version"
->
getVersion
)
}
override
def
resolveSummaryConflict
(
v1
:
Any
,
v2
:
Any
,
key
:
String
)
:
Any
=
{
(
v1
,
v2
)
match
{
case
(
v1
:
Int
,
v2
:
Int
)
=>
v1
+
v2
case
_
=>
v1
}
}
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
}
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment