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biopet.biopet
Commits
f42be845
Commit
f42be845
authored
Sep 28, 2015
by
Peter van 't Hof
Browse files
Adding summary stats
parent
6fc77a78
Changes
2
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public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
f42be845
...
...
@@ -183,12 +183,14 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
qcCmdR1
.
output
=
if
(
paired
)
new
File
(
"/dev/stdout"
)
else
fastqR1Qc
qcCmdR1
.
isIntermediate
=
paired
||
!
keepQcFastqFiles
addSummarizable
(
qcCmdR1
,
"qc_command_R1"
)
if
(
paired
)
{
val
qcCmdR2
=
new
QcCommand
(
this
,
fastqc_R2
)
qcCmdR2
.
input
=
R2_in
.
get
qcCmdR2
.
output
=
new
File
(
"/dev/stdout"
)
qcCmdR2
.
read
=
"R2"
addSummarizable
(
qcCmdR2
,
"qc_command_R2"
)
qcCmdR1
.
compress
=
false
qcCmdR2
.
compress
=
false
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
f42be845
...
...
@@ -2,6 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryQScript
,
Summarizable
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
BiopetPipe
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Gzip
,
Sickle
,
Cutadapt
}
import
nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
...
...
@@ -11,7 +12,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvan_thof on 9/22/15.
*/
class
QcCommand
(
val
root
:
Configurable
,
val
fastqc
:
Fastqc
)
extends
BiopetCommandLineFunction
{
class
QcCommand
(
val
root
:
Configurable
,
val
fastqc
:
Fastqc
)
extends
BiopetCommandLineFunction
with
Summarizable
{
val
flexiprep
=
root
match
{
case
f
:
Flexiprep
=>
f
...
...
@@ -35,6 +36,21 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
var
clip
:
Option
[
Cutadapt
]
=
None
var
trim
:
Option
[
Sickle
]
=
None
def
summaryFiles
=
Map
()
def
summaryStats
=
Map
()
override
def
addToQscriptSummary
(
qscript
:
SummaryQScript
,
name
:
String
)
:
Unit
=
{
clip
match
{
case
Some
(
job
)
=>
qscript
.
addSummarizable
(
job
,
s
"clipping_$read"
)
case
_
=>
}
trim
match
{
case
Some
(
job
)
=>
qscript
.
addSummarizable
(
job
,
s
"trimming_$read"
)
case
_
=>
}
}
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
require
(
read
!=
null
)
...
...
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