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biopet.biopet
Commits
6fb4feb5
Commit
6fb4feb5
authored
Apr 27, 2016
by
Peter van 't Hof
Browse files
Fix tinycap dir
parent
d2c438c8
Changes
8
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Inline
Side-by-side
tinycap/.gitignore
0 → 100644
View file @
6fb4feb5
target
\ No newline at end of file
tinycap/pom.xml
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6fb4feb5
<?xml version="1.0" encoding="UTF-8"?>
<!--
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.
-->
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation=
"http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
>
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.7.0-SNAPSHOT
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
<inceptionYear>
2016
</inceptionYear>
<artifactId>
TinyCap
</artifactId>
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Mapping
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Gentrap
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
org.testng
</groupId>
<artifactId>
testng
</artifactId>
<version>
6.8
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.10
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
</dependencies>
</project>
\ No newline at end of file
tinycap/src/main/resources/nl/lumc/sasc/biopet/pipelines/tinycap/tinycapFront.ssp
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6fb4feb5
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<%@ var pipeline: String %>
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>${pipeline}</td></tr>
<tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr>
<tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr>
<tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
<tr><th>Reference</th><td>${summary.getValue(pipeline, "settings", "reference", "species")} - ${summary.getValue(pipeline, "settings", "reference", "name")}</td></tr>
<tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
</tbody>
</table>
<br/>
<div class="row">
<div class="col-md-1"></div>
<div class="col-md-10">
<p>
In this web document you can find your <em><strong>${pipeline}</strong></em> pipeline report.
Different categories of data can be found in the left-side menu.
Statistics per sample and library can be accessed through the top-level menu.
Futhermore, you can view all versions of software tools used by selecting <em><a href="./Versions/index.html">Versions</a></em> from the top menu.
</p>
<p>
<small>Brought to you by <a href="https://sasc.lumc.nl" target="_blank"><abbr
title="Sequence Analysis Support Core">SASC</abbr></a> and <a
href="https://www.lumc.nl/org/klinische-genetica/" target="_blank"><abbr title="Clinical Genetics LUMC">KG</abbr></a>,
LUMC.
</small>
</p>
</div>
<div class="col-md-1"></div>
</div>
\ No newline at end of file
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala
0 → 100644
View file @
6fb4feb5
/**
* 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.tinycap
import
java.io.File
import
nl.lumc.sasc.biopet.core.annotations.
{
AnnotationGff
,
AnnotationGtf
,
AnnotationRefFlat
}
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
}
import
nl.lumc.sasc.biopet.pipelines.gentrap.measures.
{
BaseCounts
,
FragmentsPerGene
}
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import
nl.lumc.sasc.biopet.pipelines.tinycap.measures.FragmentsPerSmallRna
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
import
picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
/**
* Created by pjvan_thof on 12/29/15.
* Design based on work from Henk Buermans (e-Mir)
* Implementation by wyleung started 19/01/16
*/
class
TinyCap
(
val
root
:
Configurable
)
extends
QScript
with
MultisampleMappingTrait
with
AnnotationRefFlat
with
AnnotationGff
with
AnnotationGtf
with
Reference
{
qscript
=>
def
this
()
=
this
(
null
)
var
annotateSam
:
Boolean
=
config
(
"annotate_sam"
,
default
=
false
)
override
def
defaults
=
Map
(
"igvtoolscount"
->
Map
(
"strands"
->
"reads"
,
"includeDuplicates"
->
true
),
"merge_strategy"
->
"preprocessmergesam"
,
"keep_merged_files"
->
true
,
"mapping"
->
Map
(
"aligner"
->
"bowtie"
,
"generate_wig"
->
true
,
"skip_markduplicates"
->
true
),
"bammetrics"
->
Map
(
"wgs_metrics"
->
false
,
"rna_metrics"
->
false
,
"collectrnaseqmetrics"
->
Map
(
"strand_specificity"
->
StrandSpecificity
.
SECOND_READ_TRANSCRIPTION_STRAND
.
toString
)
),
"bowtie"
->
Map
(
"chunkmbs"
->
256
,
"seedmms"
->
3
,
"seedlen"
->
25
,
"k"
->
5
,
"best"
->
true
),
"sickle"
->
Map
(
"lengthThreshold"
->
15
),
"fastqc"
->
Map
(
"sensitiveAdapterSearch"
->
true
),
"cutadapt"
->
Map
(
"error_rate"
->
0.2
,
"minimum_length"
->
15
,
"q"
->
30
,
"default_clip_mode"
->
"both"
,
"times"
->
2
)
)
lazy
val
fragmentsPerGene
=
new
FragmentsPerGene
(
this
)
lazy
val
fragmentsPerSmallRna
=
new
FragmentsPerSmallRna
(
this
)
lazy
val
baseCounts
=
new
BaseCounts
(
this
)
def
executedMeasures
=
(
fragmentsPerGene
::
fragmentsPerSmallRna
::
baseCounts
::
Nil
)
override
def
init
=
{
super
.
init
()
executedMeasures
.
foreach
(
x
=>
x
.
outputDir
=
new
File
(
outputDir
,
"expression_measures"
+
File
.
separator
+
x
.
name
))
}
override
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
super
.
Sample
(
sampleId
)
{
override
def
addJobs
()
:
Unit
=
{
super
.
addJobs
()
preProcessBam
.
foreach
{
file
=>
executedMeasures
.
foreach
(
_
.
addBamfile
(
sampleId
,
file
))
}
}
}
override
def
summaryFile
=
new
File
(
outputDir
,
"tinycap.summary.json"
)
override
def
summaryFiles
:
Map
[
String
,
File
]
=
super
.
summaryFiles
++
Map
(
"annotation_refflat"
->
annotationRefFlat
(),
"annotationGtf"
->
annotationGtf
,
"annotationGff"
->
annotationGff
)
override
def
reportClass
:
Option
[
ReportBuilderExtension
]
=
{
val
report
=
new
TinyCapReport
(
this
)
report
.
outputDir
=
new
File
(
outputDir
,
"report"
)
report
.
summaryFile
=
summaryFile
Some
(
report
)
}
override
def
addMultiSampleJobs
=
{
super
.
addMultiSampleJobs
executedMeasures
.
foreach
(
add
)
}
}
object
TinyCap
extends
PipelineCommand
\ No newline at end of file
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapReport.scala
0 → 100644
View file @
6fb4feb5
/**
* 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.tinycap
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilderExtension
,
ReportSection
}
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
import
nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by wyleung on 4-2-16.
*/
class
TinyCapReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
def
builder
=
TinyCapReport
}
object
TinyCapReport
extends
MultisampleMappingReportTrait
{
/** Name of the report */
def
reportName
=
"TinyCap Report"
/** Front section for the report */
override
def
frontSection
:
ReportSection
=
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/tinycap/tinycapFront.ssp"
)
override
def
additionalSections
=
List
(
"Fragments per gene"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gentrap/measure_plotreport.ssp"
,
Map
(
"pipelineName"
->
pipelineName
,
"plotName"
->
"fragmentspergene"
,
"plotPath"
->
summary
.
getValue
(
"fragmentspergene"
,
"files"
,
"pipeline"
,
"fragments_per_gene_heatmap"
,
"path"
)
)),
"Fragments per microRNA"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gentrap/measure_plotreport.ssp"
,
Map
(
"pipelineName"
->
pipelineName
,
"plotName"
->
"fragmentspersmallrna"
,
"plotPath"
->
summary
.
getValue
(
"fragmentspersmallrna"
,
"files"
,
"pipeline"
,
"fragments_per_smallrna_heatmap"
,
"path"
)))
)
override
def
pipelineName
=
"tinycap"
}
tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/measures/FragmentsPerSmallRna.scala
0 → 100644
View file @
6fb4feb5
/**
* 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.tinycap.measures
import
nl.lumc.sasc.biopet.core.annotations.AnnotationGff
import
nl.lumc.sasc.biopet.extensions.HtseqCount
import
nl.lumc.sasc.biopet.pipelines.gentrap.measures.Measurement
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by wyleung on 11-2-16.
*/
class
FragmentsPerSmallRna
(
val
root
:
Configurable
)
extends
QScript
with
Measurement
with
AnnotationGff
{
def
mergeArgs
=
MergeArgs
(
List
(
1
),
2
,
numHeaderLines
=
1
,
fallback
=
"0"
)
/** Pipeline itself */
def
biopetScript
()
:
Unit
=
{
val
jobs
=
bamFiles
.
map
{
case
(
id
,
file
)
=>
// Do expression counting for miRNA and siRNA
val
job
=
new
HtseqCount
(
this
)
job
.
inputAlignment
=
file
job
.
inputAnnotation
=
annotationGff
job
.
format
=
Option
(
"bam"
)
job
.
stranded
=
Option
(
"yes"
)
job
.
featuretype
=
Option
(
"miRNA"
)
job
.
idattr
=
Option
(
"Name"
)
job
.
output
=
new
File
(
outputDir
,
s
"$id.$name.counts"
)
add
(
job
)
id
->
job
}
addMergeTableJob
(
jobs
.
values
.
map
(
_
.
output
).
toList
,
mergedTable
,
"fragments_per_smallrna"
,
s
".$name.counts"
)
addHeatmapJob
(
mergedTable
,
heatmap
,
"fragments_per_smallrna"
)
addSummaryJobs
()
}
def
mergedTable
=
new
File
(
outputDir
,
s
"$name.fragments_per_smallrna.tsv"
)
def
heatmap
=
new
File
(
outputDir
,
s
"$name.fragments_per_smallrna.png"
)
}
tinycap/src/test/resources/log4j.properties
0 → 100644
View file @
6fb4feb5
#
# 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.
#
# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger
=
ERROR, A1
# A1 is set to be a ConsoleAppender.
log4j.appender.A1
=
org.apache.log4j.ConsoleAppender
# A1 uses PatternLayout.
log4j.appender.A1.layout
=
org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern
=
%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
0 → 100644
View file @
6fb4feb5
/**
* Created by wyleung on 11-2-16.
*/
/**
* 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.tinycap
import
java.io.File
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.HtseqCount
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
class
TinyCapTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
TinyCap
=
{
new
TinyCap
()
{
override
def
configNamespace
=
"tinycap"
override
def
globalConfig
=
new
Config
(
map
)
qSettings
=
new
QSettings
qSettings
.
runName
=
"test"
}
}
@DataProvider
(
name
=
"tinyCapOptions"
)
def
tinyCapOptions
=
{
val
bool
=
Array
(
true
)
for
(
s1
<-
bool
)
yield
Array
(
""
,
s1
)
}
@Test
(
dataProvider
=
"tinyCapOptions"
)
def
testTinyCap
(
dummy
:
String
,
sample1
:
Boolean
)
:
Unit
=
{
val
map
=
{
var
m
:
Map
[
String
,
Any
]
=
TinyCapTest
.
config
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
TinyCapTest
.
sample1
,
m
)
m
}
if
(!
sample1
)
{
// When no samples
intercept
[
IllegalArgumentException
]
{
initPipeline
(
map
).
script
()
}
}
val
pipeline
=
initPipeline
(
map
)
pipeline
.
script
()
// expect 2 instances of HtSeqCount, one for mirna.gff other for transcripts.gtf
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
HtseqCount
])
shouldBe
2
}
// remove temporary run directory all tests in the class have been run
@AfterClass
def
removeTempOutputDir
()
=
{
FileUtils
.
deleteDirectory
(
TinyCapTest
.
outputDir
)
}
}
object
TinyCapTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
val
r1
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R1.fq.gz"
)
Files
.
touch
(
r1
)
val
bam
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"bamfile.bam"
)
Files
.
touch
(
bam
)
val
referenceFasta
=
new
File
(
outputDir
,
"ref.fa"
)
Files
.
touch
(
referenceFasta
)
val
referenceFastaDict
=
new
File
(
outputDir
,
"ref.dict"
)
Files
.
touch
(
referenceFastaDict
)
val
bowtieIndex
=
new
File
(
outputDir
,
"ref.1.ebwt"
)
Files
.
touch
(
bowtieIndex
)
val
annotationGFF
=
new
File
(
outputDir
,
"annot.gff"
)
val
annotationGTF
=
new
File
(
outputDir
,
"annot.gtf"
)
val
annotationRefflat
=
new
File
(
outputDir
,
"annot.refflat"
)
Files
.
touch
(
annotationGFF
)
Files
.
touch
(
annotationGTF
)
Files
.
touch
(
annotationRefflat
)
val
config
=
Map
(
"output_dir"
->
outputDir
,
"reference_fasta"
->
(
referenceFasta
.
getAbsolutePath
),
"bowtie_index"
->
(
bowtieIndex
.
getAbsolutePath
),
"annotation_gff"
->
annotationGFF
,
"annotation_gtf"
->
annotationGTF
,
"annotation_refflat"
->
annotationRefflat
,
"md5sum"
->
Map
(
"exe"
->
"test"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
"sickle"
->
Map
(
"exe"
->
"test"
),
"cutadapt"
->
Map
(
"exe"
->
"test"
),
"bowtie"
->
Map
(
"exe"
->
"test"
),
"htseqcount"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
),
"wigtobigwig"
->
Map
(
"exe"
->
"test"
)
)
val
sample1
=
Map
(
"samples"
->
Map
(
"sample1"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
r1
.
getAbsolutePath
)
)
)))
}
\ No newline at end of file
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