Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
bb9a3e4e
Commit
bb9a3e4e
authored
Mar 03, 2017
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Switch templates to scalaz
parent
18b8594a
Changes
9
Hide whitespace changes
Inline
Side-by-side
Showing
9 changed files
with
38 additions
and
21 deletions
+38
-21
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
...umc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
+3
-1
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
...ces/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
+3
-1
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
...s/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
+3
-1
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
.../lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
+3
-1
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
...nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
+3
-1
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
...n/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
+4
-3
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
.../sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
+6
-4
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp
...c/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp
+5
-3
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
.../sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
+8
-6
No files found.
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
...
...
@@ -87,7 +89,7 @@
"Duplicates" -> List("flagstats", "Duplicates"),
"NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment")
)
val results = summary.getStatKeys(runId,
Right("bammetrics"), Some(Right("bamstats")), sample = Some(Left(sample.id)), library = libId.map(Left(_)
), keyValues = statsPaths)
val results = summary.getStatKeys(runId,
"bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left
), keyValues = statsPaths)
val total = results("All").getOrElse(0L).asInstanceOf[Long]
val mapped = results("Mapped").getOrElse(0L).asInstanceOf[Long]
val duplicates = results("Duplicates").getOrElse(0L).asInstanceOf[Long]
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
...
...
@@ -82,7 +84,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("clipping", "general", x)).toMap
val results = summary.getStatKeys(runId,
Right("bammetrics"), Some(Right("bamstats")), sample = Some(Left(sample.id)), library = libId.map(Left(_)
), keyValues = statsPaths)
val results = summary.getStatKeys(runId,
"bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left
), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
...
...
@@ -84,7 +86,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
val results = summary.getStatKeys(runId,
Right("bammetrics"), Some(Right("CollectInsertSizeMetrics")), sample = Some(Left(sample.id)), library = libId.map(Left(_)
), keyValues = statsPaths)
val results = summary.getStatKeys(runId,
"bammetrics".right, Some("CollectInsertSizeMetrics".right), sample = Some(sample.id.left), library = libId.map(_.left
), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
...
...
@@ -83,7 +85,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("mapping_quality", "general", x)).toMap
val results = summary.getStatKeys(runId,
Right("bammetrics"), Some(Right("bamstats")), sample = Some(Left(sample.id)), library = libId.map(Left(_)
), keyValues = statsPaths)
val results = summary.getStatKeys(runId,
"bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left
), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
...
...
@@ -73,7 +75,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("metrics", x)).toMap
val results = summary.getStatKeys(runId,
Right("bammetrics"), Some(Right("wgs")), sample = Some(Left(sample.id)), library = libId.map(Left(_)
), keyValues = statsPaths)
val results = summary.getStatKeys(runId,
"bammetrics".right, Some("wgs".right), sample = Some(sample.id.left), library = libId.map(_.left
), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
...
...
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
View file @
bb9a3e4e
...
...
@@ -2,7 +2,8 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var rootPath: String %>
<%@ var pipeline: String %>
...
...
@@ -10,7 +11,7 @@
#{
val settings = summary.getSettingKeys(runId,
Right(pipeline)
,
val settings = summary.getSettingKeys(runId,
pipeline.right
,
keyValues = Map(
"contigs" -> List("reference", "contigs"),
"species" -> List("reference", "species"),
...
...
@@ -18,7 +19,7 @@
))
val contigs = settings.getOrElse("contigs", Some(Map())).getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
val referenceFile = Await.result(summary.getFile(runId,
Right(pipeline)
, None, None, None, key = "referenceFasta"), Duration.Inf)
val referenceFile = Await.result(summary.getFile(runId,
pipeline.right
, None, None, None, key = "referenceFasta"), Duration.Inf)
}#
<table class="table">
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
View file @
bb9a3e4e
...
...
@@ -5,6 +5,8 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var runId: Int %>
<%@ var sampleId: Option[Int] = None %>
...
...
@@ -18,7 +20,7 @@
#{
val samples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val settings = summary.getSettingsForLibraries(runId,
Right("flexiprep")
, keyValues = Map(
val settings = summary.getSettingsForLibraries(runId,
"flexiprep".right
, keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
...
...
@@ -26,7 +28,7 @@
val librariesCount = libraries.size
val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
summary.getSettingKeys(runId,
Right("flexiprep"), None, sampleId.map(Left(_)), libId.map(Left(_)
), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
summary.getSettingKeys(runId,
"flexiprep".right, None, sampleId.map(_.left), libId.map(_.left
), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
}#
#if (showIntro)
...
...
@@ -137,8 +139,8 @@
#if (read == "R2") </tr><tr> #end
#{
val statsPaths = Map("num_total" -> List("bases", "num_total"))
val seqstatStats = summary.getStatKeys(runId,
Right("flexiprep"), Some(Right("seqstat_" + read)), sample = Some(Left(sample.id)), library = Some(Left(lib.id)
), keyValues = statsPaths)
val seqstatQcStats = summary.getStatKeys(runId,
Right("flexiprep"), Some(Right("seqstat_" + read + "_qc")), sample = Some(Left(sample.id)), library = Some(Left(lib.id)
), keyValues = statsPaths)
val seqstatStats = summary.getStatKeys(runId,
"flexiprep".right, Some(("seqstat_" + read).right), sample = Some(sample.id.left), library = Some(lib.id.left
), keyValues = statsPaths)
val seqstatQcStats = summary.getStatKeys(runId,
"flexiprep".right, Some(("seqstat_" + read + "_qc").right), sample = Some(sample.id.left), library = Some(lib.id.left
), keyValues = statsPaths)
val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong
val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp
View file @
bb9a3e4e
...
...
@@ -5,6 +5,8 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var runId: Int %>
<%@ var sampleId: Option[Int] %>
...
...
@@ -12,7 +14,7 @@
<%@ var plot: String %>
<%@ var outputDir: File %>
#{
val settings = summary.getSettingKeys(runId,
Right("flexiprep"), None, sampleId.map(Left(_)), libId.map(Left(_)
), keyValues = Map(
val settings = summary.getSettingKeys(runId,
"flexiprep".right, None, sampleId.map(_.left), libId.map(_.left
), keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
val paired: Boolean = settings("paired") == Some(true)
...
...
@@ -20,7 +22,7 @@
val skipTrim: Boolean = settings("skip_trim") == Some(true)
def getPlot(read:String) = {
val file = Await.result(summary.getFile(runId,
Right("flexiprep"), Some(Right(read)), sampleId.map(Left(_)), libId.map(Left(_)
), plot), Duration.Inf)
val file = Await.result(summary.getFile(runId,
"flexiprep".right, Some(read.right), sampleId.map(_.left), libId.map(_.left
), plot), Duration.Inf)
file.collect {
case path => {
val file = new File(path.path.toString)
...
...
@@ -32,7 +34,7 @@
}
def plotAvailable(read:String) = {
val file = Await.result(summary.getFile(runId,
Right("flexiprep"), Some(Right(read)), sampleId.map(Left(_)), libId.map(Left(_)
), plot), Duration.Inf)
val file = Await.result(summary.getFile(runId,
"flexiprep".right, Some(read.right), sampleId.map(_.left), libId.map(_.left
), plot), Duration.Inf)
file.map(x => new File(x.path).exists()).getOrElse(false)
}
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @
bb9a3e4e
...
...
@@ -4,6 +4,8 @@
#import(scala.concurrent.duration.Duration)
#import(java.io.File)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %>
<%@ var runId: Int %>
<%@ var sampleId: Option[Int] = None %>
...
...
@@ -17,7 +19,7 @@
#{
val samples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val settings = summary.getSettingsForLibraries(runId,
Right("flexiprep")
, keyValues = Map(
val settings = summary.getSettingsForLibraries(runId,
"flexiprep".right
, keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
...
...
@@ -25,7 +27,7 @@
val librariesCount = libraries.size
val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
summary.getSettingKeys(runId,
Right("flexiprep"), None, sampleId.map(Left(_)), libId.map(Left(_)
), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
summary.getSettingKeys(runId,
"flexiprep".right, None, sampleId.map(_.left), libId.map(_.left
), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
}#
...
...
@@ -142,15 +144,15 @@
#if (read == "R2") </tr><tr> #end
#{
val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val seqstatStats = summary.getStatKeys(runId,
Right("flexiprep"), Some(Right("seqstat_" + read)), sample = Some(Left(sample.id)), library = Some(Left(lib.id)
), keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatKeys(runId,
Right("flexiprep"), Some(Right("seqstat_" + read + "_qc")), sample = Some(Left(sample.id)), library = Some(Left(lib.id)
), keyValues = seqstatPaths)
val seqstatStats = summary.getStatKeys(runId,
"flexiprep".right, Some(("seqstat_" + read).right), sample = Some(sample.id.left), library = Some(lib.id.left
), keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatKeys(runId,
"flexiprep".right, Some(("seqstat_" + read + "_qc").right), sample = Some(sample.id.left), library = Some(lib.id.left
), keyValues = seqstatPaths)
val clippingPaths = Map("num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"),
"num_reads_discarded_too_long" -> List("num_reads_discarded_too_long"))
val clippingStats = summary.getStatKeys(runId,
Right("flexiprep"), Some(Right("clipping_" + read)), sample = Some(Left(sample.id)), library = Some(Left(lib.id)
), keyValues = clippingPaths)
val clippingStats = summary.getStatKeys(runId,
"flexiprep".right, Some(("clipping_" + read).right), sample = Some(sample.id.left), library = Some(lib.id.left
), keyValues = clippingPaths)
val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_" + read))
val trimmingStats = summary.getStatKeys(runId,
Right("flexiprep"), Some(Right("trimming")), sample = Some(Left(sample.id)), library = Some(Left(lib.id)
), keyValues = trimmingPaths)
val trimmingStats = summary.getStatKeys(runId,
"flexiprep".right, Some("trimming".right), sample = Some(sample.id.left), library = Some(lib.id.left
), keyValues = trimmingPaths)
val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong
val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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