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biopet.biopet
Commits
3c616b75
Commit
3c616b75
authored
Aug 25, 2014
by
Peter van 't Hof
Browse files
Moved scripts to general package
parent
f3276d72
Changes
12
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
3c616b75
package
nl.lumc.sasc.biopet.pipelines.bammetrics
import
nl.lumc.sasc.biopet.
pipelines.bammetrics.
scripts.CoverageStats
import
nl.lumc.sasc.biopet.scripts.CoverageStats
import
org.broadinstitute.gatk.queue.QScript
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
java.io.File
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
3c616b75
...
...
@@ -6,7 +6,7 @@ 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.
{
Gzip
,
Pbzip2
,
Md5sum
,
Zcat
}
import
nl.lumc.sasc.biopet.
pipelines.flexiprep.
scripts._
import
nl.lumc.sasc.biopet.scripts._
class
Flexiprep
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
View file @
3c616b75
...
...
@@ -3,8 +3,7 @@ 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.Md5sum
import
nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.
{
FastqSync
,
Seqstat
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.Seqstat
import
nl.lumc.sasc.biopet.scripts.
{
FastqSync
,
Seqstat
}
import
org.broadinstitute.gatk.queue.function.InProcessFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
pipelines/bammetrics/
scripts/CoverageStats.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
View file @
3c616b75
package
nl.lumc.sasc.biopet.
pipelines.bammetrics.
scripts
package
nl.lumc.sasc.biopet.scripts
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
pipelines/flexiprep/
scripts/FastqSync.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/FastqSync.scala
View file @
3c616b75
package
nl.lumc.sasc.biopet.
pipelines.flexiprep.
scripts
package
nl.lumc.sasc.biopet.scripts
import
java.io.File
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
pipelines/flexiprep/
scripts/FastqcToContams.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/FastqcToContams.scala
View file @
3c616b75
package
nl.lumc.sasc.biopet.
pipelines.flexiprep.
scripts
package
nl.lumc.sasc.biopet.scripts
import
java.io.File
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
pipelines/flexiprep/
scripts/Seqstat.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/Seqstat.scala
View file @
3c616b75
package
nl.lumc.sasc.biopet.
pipelines.flexiprep.
scripts
package
nl.lumc.sasc.biopet.scripts
import
java.io.File
...
...
biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/
pipelines/bammetrics/
scripts/bedtools_cov_stats.py
→
biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/scripts/bedtools_cov_stats.py
View file @
3c616b75
File moved
biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/
pipelines/flexiprep/
scripts/fastqc_contam.py
→
biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/scripts/fastqc_contam.py
View file @
3c616b75
File moved
biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/
pipelines/flexiprep/
scripts/pyfastqc/__init__.py
→
biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/scripts/pyfastqc/__init__.py
View file @
3c616b75
File moved
biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/
pipelines/flexiprep/
scripts/seq_stat.py
→
biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/scripts/seq_stat.py
View file @
3c616b75
File moved
biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/
pipelines/flexiprep/
scripts/sync_paired_end_reads.py
→
biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/scripts/sync_paired_end_reads.py
View file @
3c616b75
File moved
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