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biopet.biopet
Commits
41fa137b
Commit
41fa137b
authored
Aug 11, 2014
by
Peter van 't Hof
Browse files
Switch to md5sum
parent
b94b634c
Changes
2
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
41fa137b
...
...
@@ -5,7 +5,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Ln
,
Pbzip2
,
Sha1
sum
,
Zcat
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Ln
,
Pbzip2
,
Md5
sum
,
Zcat
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
class
Flexiprep
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
...
...
@@ -89,9 +89,9 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
outputFiles
+=
(
"fastqc_R1"
->
fastqc_R1
.
output
)
outputFiles
+=
(
"contams_R1"
->
getContams
(
fastqc_R1
,
R1_name
))
val
sha1
sum_R1
=
Sha1
sum
(
this
,
outputFiles
(
"fastq_
input_R1
"
)
,
outputDir
)
add
(
sha1
sum_R1
)
summary
.
add
Sha1sum
(
sha1
sum_R1
,
R2
=
false
,
after
=
false
)
val
md5
sum_R1
=
Md5
sum
(
this
,
input_R1
,
outputDir
)
add
(
md5
sum_R1
)
summary
.
add
Md5sum
(
md5
sum_R1
,
R2
=
false
,
after
=
false
)
if
(
paired
)
{
fastqc_R2
=
Fastqc
(
this
,
input_R2
,
outputDir
+
"/"
+
R2_name
+
".fastqc/"
)
...
...
@@ -100,9 +100,9 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
outputFiles
+=
(
"fastqc_R2"
->
fastqc_R2
.
output
)
outputFiles
+=
(
"contams_R2"
->
getContams
(
fastqc_R2
,
R2_name
))
val
sha1
sum_R2
=
Sha1
sum
(
this
,
outputFiles
(
"fastq_
input_R2
"
)
,
outputDir
)
add
(
sha1
sum_R2
)
summary
.
add
Sha1sum
(
sha1
sum_R2
,
R2
=
true
,
after
=
false
)
val
md5
sum_R2
=
Md5
sum
(
this
,
input_R2
,
outputDir
)
add
(
md5
sum_R2
)
summary
.
add
Md5sum
(
md5
sum_R2
,
R2
=
true
,
after
=
false
)
}
}
...
...
@@ -253,13 +253,13 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
if
(
paired
)
outputFiles
+=
(
"output_R2"
->
R2
)
if
(!
skipTrim
||
!
skipClip
)
{
val
sha1
sum_R1
=
Sha1
sum
(
this
,
R1
,
outputDir
)
add
(
sha1
sum_R1
)
summary
.
add
Sha1sum
(
sha1
sum_R1
,
R2
=
false
,
after
=
true
)
val
md5
sum_R1
=
Md5
sum
(
this
,
R1
,
outputDir
)
add
(
md5
sum_R1
)
summary
.
add
Md5sum
(
md5
sum_R1
,
R2
=
false
,
after
=
true
)
if
(
paired
)
{
val
sha1
sum_R2
=
Sha1
sum
(
this
,
R2
,
outputDir
)
add
(
sha1
sum_R2
)
summary
.
add
Sha1sum
(
sha1
sum_R2
,
R2
=
true
,
after
=
true
)
val
md5
sum_R2
=
Md5
sum
(
this
,
R2
,
outputDir
)
add
(
md5
sum_R2
)
summary
.
add
Md5sum
(
md5
sum_R2
,
R2
=
true
,
after
=
true
)
}
fastqc_R1_after
=
Fastqc
(
this
,
outputFiles
(
"output_R1"
),
outputDir
+
"/"
+
R1_name
+
".qc.fastqc/"
)
add
(
fastqc_R1_after
)
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
View file @
41fa137b
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.
Sha1
sum
import
nl.lumc.sasc.biopet.extensions.
Md5
sum
import
nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.
{
FastqSync
,
Seqstat
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.Seqstat
import
org.broadinstitute.gatk.queue.function.InProcessFunction
...
...
@@ -36,10 +36,10 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
var
chunks
:
Map
[
String
,
Chunk
]
=
Map
()
var
sha1R1
:
Sha1
sum
=
_
var
sha1R2
:
Sha1
sum
=
_
var
sha1
R1after
:
Sha1
sum
=
_
var
sha1
R2after
:
Sha1
sum
=
_
var
md5R1
:
Md5
sum
=
_
var
md5R2
:
Md5
sum
=
_
var
md5
R1after
:
Md5
sum
=
_
var
md5
R2after
:
Md5
sum
=
_
var
fastqcR1
:
Fastqc
=
_
var
fastqcR2
:
Fastqc
=
_
...
...
@@ -59,13 +59,13 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
return
fastqc
}
def
add
Sha1sum
(
sha1
sum
:
Sha1
sum
,
R2
:
Boolean
=
false
,
after
:
Boolean
=
false
)
:
Sha1
sum
=
{
if
(!
R2
&&
!
after
)
this
.
sha1
R1
=
sha1
sum
else
if
(!
R2
&&
after
)
this
.
sha1
R1after
=
sha1
sum
else
if
(
R2
&&
!
after
)
this
.
sha1
R2
=
sha1
sum
else
if
(
R2
&&
after
)
this
.
sha1
R2after
=
sha1
sum
deps
::=
sha1
sum
.
output
return
sha1
sum
def
add
Md5sum
(
md5
sum
:
Md5
sum
,
R2
:
Boolean
=
false
,
after
:
Boolean
=
false
)
:
Md5
sum
=
{
if
(!
R2
&&
!
after
)
this
.
md5
R1
=
md5
sum
else
if
(!
R2
&&
after
)
this
.
md5
R1after
=
md5
sum
else
if
(
R2
&&
!
after
)
this
.
md5
R2
=
md5
sum
else
if
(
R2
&&
after
)
this
.
md5
R2after
=
md5
sum
deps
::=
md5
sum
.
output
return
md5
sum
}
def
addSeqstat
(
seqstat
:
Seqstat
,
R2
:
Boolean
=
false
,
after
:
Boolean
=
false
,
chunk
:
String
=
""
)
:
Seqstat
=
{
...
...
@@ -102,7 +102,7 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
// format: OFF
override
def
run
{
logger
.
debug
(
"Start"
)
sha1
Summary
()
md5
Summary
()
val
summary
=
(
"samples"
:=
(
flexiprep
.
sampleName
:=
(
"runs"
:=
(
flexiprep
.
libraryName
:=
(
...
...
@@ -116,10 +116,10 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
(
"clipping"
:=?
clipstatSummary
)
->?:
(
"trimming"
:=?
trimstatSummary
)
->?:
jEmptyObject
))
->:
(
"resourses"
:=
((
"raw_R1"
:=
getResourses
(
fastqcR1
,
sha1
R1
))
->:
(
"raw_R2"
:?=
getResourses
(
fastqcR2
,
sha1
R2
))
->?:
(
"proc_R1"
:?=
getResourses
(
fastqcR1after
,
sha1
R1after
))
->?:
(
"proc_R2"
:?=
getResourses
(
fastqcR2after
,
sha1
R2after
))
->?:
(
"resourses"
:=
((
"raw_R1"
:=
getResourses
(
fastqcR1
,
md5
R1
))
->:
(
"raw_R2"
:?=
getResourses
(
fastqcR2
,
md5
R2
))
->?:
(
"proc_R1"
:?=
getResourses
(
fastqcR1after
,
md5
R1after
))
->?:
(
"proc_R2"
:?=
getResourses
(
fastqcR2after
,
md5
R2after
))
->?:
jEmptyObject
))
->:
jEmptyObject
))->:
jEmptyObject
)->:
jEmptyObject
)->:
jEmptyObject
)
->:
jEmptyObject
// format: ON
...
...
@@ -160,11 +160,11 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
jEmptyObject
)
}
def
sha1
Summary
()
{
val
R1_raw
=
sha1
Summary
(
sha1
R1
)
val
R2_raw
=
sha1
Summary
(
sha1
R2
)
val
R1_proc
=
sha1
Summary
(
sha1
R1after
)
val
R2_proc
=
sha1
Summary
(
sha1
R2after
)
def
md5
Summary
()
{
val
R1_raw
=
md5
Summary
(
md5
R1
)
val
R2_raw
=
md5
Summary
(
md5
R2
)
val
R1_proc
=
md5
Summary
(
md5
R1after
)
val
R2_proc
=
md5
Summary
(
md5
R2after
)
if
(!
R1_raw
.
isEmpty
)
resourses
+=
(
"fastq_R1_raw"
->
R1_raw
.
get
)
if
(!
R2_raw
.
isEmpty
)
resourses
+=
(
"fastq_R2_raw"
->
R2_raw
.
get
)
...
...
@@ -172,15 +172,15 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
if
(!
R2_proc
.
isEmpty
)
resourses
+=
(
"fastq_R2_proc"
->
R2_proc
.
get
)
}
def
sha1
Summary
(
sha1
sum
:
Sha1
sum
)
:
Option
[
Json
]
=
{
if
(
sha1
sum
==
null
)
return
None
else
return
Option
(
sha1
sum
.
getSummary
)
def
md5
Summary
(
md5
sum
:
Md5
sum
)
:
Option
[
Json
]
=
{
if
(
md5
sum
==
null
)
return
None
else
return
Option
(
md5
sum
.
getSummary
)
}
def
getResourses
(
fastqc
:
Fastqc
,
sha1sum
:
Sha1
sum
)
:
Option
[
Json
]
=
{
if
(
fastqc
==
null
||
sha1
sum
==
null
)
return
None
def
getResourses
(
fastqc
:
Fastqc
,
md5sum
:
Md5
sum
)
:
Option
[
Json
]
=
{
if
(
fastqc
==
null
||
md5
sum
==
null
)
return
None
val
fastqcSum
=
fastqcSummary
(
fastqc
).
get
return
Option
((
"fastq"
:=
sha1
Summary
(
sha1
sum
))
->:
fastqcSum
)
return
Option
((
"fastq"
:=
md5
Summary
(
md5
sum
))
->:
fastqcSum
)
}
def
fastqcSummary
(
fastqc
:
Fastqc
)
:
Option
[
Json
]
=
{
...
...
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